The Mongol leader Genghis Khan united the various Mongol-speaking tribes of the steppes and in 1215 conquered northern China. He divided his empire into four kingdoms, each ruled by one of his sons. His grandson Kublai Khan (r. 1260-94), ruler of the eastern Great Khanate, finally defeated the Southern Song in 1279 and proclaimed himself emperor of the Yuan dynasty. China now became part of a vast empire which stretched from the East China Sea across Asia as far as Russia, the Ukraine, and Baghdad. Two capitals were maintained at Dadu or Khanbalik (present-day Beijing) and Yuanshangdu (Xanadu). The Silk Routes opened once more, connecting China to the Middle East and Medieval Europe. Direct contact was now made for the first time between the Mongol court and European diplomats, Franciscan missionaries, and merchants. According to the writings of Marco Polo, the Italian merchant spent 21 years in the service of Kublai and his court.

The Mongols ruled through a form of military government, in contrast to the bureaucratic civil service established by the Chinese. Although Chinese and Mongol languages were both used for official business, the Chinese were not encouraged to take up official posts. Muslims from Central and Western Asia took their place, and the Chinese increasingly retreated from official life.

As there were no clear rules for succession, civil war broke out in 1328 between Mongol nobles. The secret societies of the Red Turbans and the White Lotus led peasant rebellions and in 1368 General Zhu Yuanzhang forced the Mongols out of China, becoming the first emperor of the Ming dynasty.