Toghun Temür was born to when he stayed Central Asia in evacuation. Toghun Temür's mother was a daughter of the chief of the Qarluq tribe, whose rank was not high in the court.
Following the civil war broke out after Yesün Temür Khan's death in 1328, he attended his father Kuśala and entered Shangdu via Mongolia. But after Kuśala died and Kuśala's younger brother was restored to the throne, he was kept from the court. He was banished to Goryeo and then to Guangxi.
In 1332 when Tugh Temür died, his widow Budashiri Khatun respected his will to make Kuśala's son succeed the throne instead of his son El Tegüs. But it was not Toghun Temür but his younger brother who became the emperor. Rinchinbal died in two months, and the de facto ruler El Temür attempted to install El Tegüs again, but it was rejected by Budashiri. As a result, Toghun Temür was summoned back from Guangxi.
El Temür feared that Toghun Temür, who was too mature to be a puppet, would take against him since he was suspected of the assassination on Toghun Temür's father Kuśala. The enthronement of Toghun Temür was postponed for six months by El Temür. He managed to succeed to the throne in 1333 when El Temür died.
Struggles during the early reign
Toghun Temür appointed his nephew El Tegüs as Crown Prince, and was in ward to El Tegüs's mother Budashiri. But he was controlled by warlords even after El Temür's death. Among them, became as powerful as El Temür had been. He served as minister of the Secretariat and crushed a rebellion by El Temür's son.
As he was grew, he came to disfavor Bayan's autocratic rule. In 1340 he allied Bayan's nephew Toghtogha, who was in discord with Bayan, and banished Bayan by coup. He also kicked El Tegüs and Budashiri out of the court. He managed to purge officials that had dominated the administration, but it only resulted in another dictatorship, that of Toghtogha and his father Majartai. In 1347 he drove them into Gangsu with assistance from former officers of Kuśala and . But he called Toghtogha back in 1349. All he could do was to back up one side of warlords over power.
While the central government waged endless power struggles, people in the countryside suffered from frequent natural disasters; droughts, floods and the ensuing famines. The government's lack of policy led to a loss of the support from people. Illicit salt dealers who were disaffected with the government's salt monopoly raised a rebellion in 1348. It triggered many revolts around the empire. Among them, the Red Turban Rebellion, which started in 1351, grew into a nationwide turmoil.
In around 1338, Sultan Muhammad bin Tughluq of Delhi Sultanate appointed Moroccan traveller Ibn Battuta an ambassador to the Mongol court of Togan Temur in China. The gifts he was to take included 200 Hindu slaves. On the Doab plain they were attacked by Hindu insurgents; the imperial cavalry killed all 4,000 of them while losing 78 men, according to Battuta, who was separated, captured, and barely escaped being killed by brigands. Battuta also luckily escaped to China.
Disorder during the late reign
In 1354, when Toghtogha led a large army to crush the Red Turban rebels, Toghun Temür suddenly dismissed him for fear of betrayal. It resulted in Toghun Temür's restoration of power on the one hand and a rapid weakening of the central government on the other. He had no choice but to rely on local warlords' military.
He gradually lost his interest in politics and ceased to intervene political struggles. His son Ayushiridar, who became Crown Prince in 1353, attempted to seize power and came to conflict with Toghun Temür's aides who dominated politics instead of the khan. Toghun Temür was unable to conciliate the dispute. In 1364 the Shangxi-based warlord Bolad Temür occupied Dadu and expelled the Crown Prince from the winter base. In alliance with the Henan-based warlord K&, Ayushiridar defeated Bolad Temür in the next year. This internal struggle resulted in further weakening of political and military power of the central government.
Retreat to the north
Unifying rebel groups in Southern China and establishing the Ming Dynasty, Zhu Yuanzhang conducted military expeditions to Northern China and defeated the Yuan army in 1368. When Köke Temür lost battles against Ming General Xu Da and the Ming troops approached Hebei, Toghun Temür gave up Dadu and fled to the summer base Shangdu.
In 1369 when Shangdu also fell under the Ming's occupation, Toghun Temür fled northward to Yingchang, which was located in southern Mongolia. He died there in 1370 and his son Ayushiridara succeeded to the throne.
At the time of his death, the Mongolia-based empire maintained its influence, stretching the domination from the Sea of Japan to Altai Mountains. There were also pro-Yuan, anti-Ming forces in Yunnan and Guizhou. Even though its control over China had not been stable yet, the Ming considered that the Yuan lost the Mandate of Heaven when it abandoned Dadu, and that the Yuan was overthrown in 1368. The Ming did not treat Toghun Temür after 1368 and his successor Ayushiridar as legitimate emperors.
The Ming gave Toghun Temür the posthumous name ''Shundi'', which implied that he followed the Mandate of Heaven ceded emperorship to the Ming. But the Yuan gave their own temple name Huizong to him.
Even after Toghun Temür, there was still Mongol resistance to the Ming. In southwestern China, Basalawarmi, the self-styled "Prince of Liang", established a Mongol resistance movement in Yunnan and Guizhou that was not put down until 1381. In the north, Chinggisid khans ruled Mongolia and claimed succession to the Mongol Empire. Historians called the Yuan Dynasty after Toghun Temür the Northern Yuan.
Mongolian chronicles such as the Erdeni-yin tobchi include a poem known as the ''Lament of Toghun Temür''. It deals with his grieving after the loss of Dadu.