The division of the Mongol Empire began after Möngke Khan died in 1259 in the siege of Diaoyu Castle with no declared successor, precipitating infighting between members of the Tolui family line for the title of khagan that escalated into the Toluid Civil War. This civil war, along with the Berke–Hulagu war and the subsequent Kaidu–Kublai war, greatly weakened the authority of the great khan over the entirety of the Mongol Empire, and the empire fractured into four khanates: the Golden Horde in Eastern Europe, the Chagatai Khanate in Central Asia, the Ilkhanate in Southwest Asia, and the Yuan dynasty^{[lower-alpha 1]} in East Asia based in modern-day Beijing – although the Yuan emperors held the nominal title of khagan of the empire.

The four divisions each pursued their own interests and objectives and fell at different times. Most of the western khanates did not recognize Kublai as Great Khan. Although some of them still asked Kublai to confirm the enthronement of their new regional khans,^[5] the four khanates were functionally independent sovereign states.^[6] The Ilkhanate and the Yuan dynasty had close diplomatic relations, and shared scientific and cultural knowledge, but military cooperation between all four Mongol khanates would never occur again — the united Mongol Empire had disintegrated.^[6]

Möngke Khan's brother Hulagu Khan broke off his successful military advance into Syria, withdrawing the bulk of his forces to Mughan and leaving only a small contingent under his general Kitbuqa. The opposing forces in the region, the Christian Crusaders and Muslim Mamluks, both recognizing that the Mongols were the greater threat, took advantage of the weakened state of the Mongol army and engaged in an unusual passive truce with each other.^[7]

In 1260, the Mamluks advanced from Egypt, being allowed to camp and resupply near the Christian stronghold of Acre, and engaged Kitbuqa's forces just north of Galilee, at the Battle of Ain Jalut. The Mongols were defeated, and Kitbuqa was executed. This pivotal battle marked the western limit for Mongol expansion, as the Mongols were never again able to make any serious military advances farther than Syria.^[7]

In a separate part of the empire, another brother of Hulagu and Möngke, Kublai, heard of the great khan's death at the Huai River in China proper. Rather than returning to the capital, he continued his advance into Wuchang, near the Yangtze River. Their younger brother Ariq Böke took advantage of the absence of Hulagu and Kublai, and used his position at the capital to win the title of great khan (khagan) for himself, with representatives of all the family branches proclaiming him as the leader at the kurultai in Karakorum. When Kublai learned of this, he summoned his own kurultai at Kaiping, where virtually all the senior princes and great noyans resident in North China and Manchuria supported his own candidacy over that of Ariq Böke.

Battles ensued between the armies of Kublai and those of his brother Ariq Böke, which included forces still loyal to Möngke's previous administration. Kublai's army easily eliminated Ariq Böke's supporters and seized control of the civil administration in southern Mongolia. Further challenges took place from their cousins, the Chagataids.^{[8][full citation needed][9][10]} Kublai sent Abishka, a Chagataid prince loyal to him, to take charge of Chagatai's realm. However, Ariq Böke captured and then executed Abishka, having his own man Alghu crowned there instead. Kublai's new administration blockaded Ariq Böke in Mongolia to cut off food supplies, causing a famine. Karakorum fell quickly to Kublai, but Ariqboke rallied and retook the capital in 1261.^[8][9][10]

In the southwestern Ilkhanate, Hulagu was loyal to his brother Kublai, but clashes with their cousin Berke, the ruler of the Golden Horde in the northwestern part of the empire, began in 1262. The suspicious deaths of Jochid princes in Hulagu's service, unequal distribution of war booty, and Hulagu's massacres of the Muslims increased the anger of Berke, who considered supporting a rebellion of the Georgian Kingdom against Hulagu's rule in 1259–1260.^{[11][page needed]} Berke also forged an alliance with the Egyptian Mamluks against Hulagu and supported Kublai's rival claimant, Ariqboke.^[12]

Hulagu died on February 8, 1265. Berke sought to take advantage and invade Hulagu's realm, but he died along the way, and a few months later, Alghu Khan of the Chagatai Khanate died as well. Kublai named Hulagu's son Abaqa as a new ilkhan, and Abaqa sought foreign alliances, such as attempting to form a Franco-Mongol alliance with the Europeans against the Egyptian Mamluks. Kublai nominated Batu's grandson Möngke Temür to lead the Golden Horde.^[13] Ariqboqe surrendered to Kublai at Shangdu on August 21, 1264.^{[14][full citation needed]}

The establishment of the Yuan dynasty (1271–1368) by Kublai (Emperor Shizu) accelerated the fragmentation of the Mongol Empire. The Mongol Empire fractured into four khanates. Two of these, the Yuan dynasty and the Ilkhanate, were ruled by the line of Tolui. The Golden Horde was founded by the line of Jochi, while the Chagatai Khanate was founded by Chagatai. In 1304, a peace treaty among the khanates established the nominal supremacy of the Yuan dynasty over the western khanates. However, this supremacy was based on nothing like the same foundations as that of the earlier khagans. Conflicts such as border clashes among them continued; for example, the Esen Buqa–Ayurbarwada war occurred between the Chagatai Khanate and the Ilkhanate in the 1310s. The four khanates continued to function as separate states and fell at different times.