The fall of the Mongol Empire triggered a serious crisis in Mongolian society. This period is known as "the age of petty rulers" in historiography. In fact, the rulers of Mongolia after 1368 reigned for brief periods and faced constant turmoil with the nobility. The khan lost much of his power. Local lords began to assert autonomy in their affairs. The ancient Mongol nation began to disintegrate.

The Oirads broke away and formed their own monarchy. Mongolia split into eastern and western regions. The eastern part further divided into inner and outer territories. The Oirads remained quite active and occasionally launched incursions into Central Asia.

The Mongolian language itself fragmented into several distinct dialects, which later evolved into separate languages. However, the 15th-17th centuries were marked by notable disciples and poets. For instance, Prince Tsogt was not merely a warrior but also a poet and philosopher.

Buddhism arrived in Mongolia in the 16th century. In 1572, Khan Altan converted to Buddhism, thus rejecting the old shamanic beliefs. Buddhism brought to the Mongols literature, philosophy, theology, and natural sciences.

The khan's supremacy was severely limited in post-imperial Mongolia. Twenty-two khans ruled Mongolia between 1370 and 1634. An Oirad prince seized the throne in 1450, breaking the tradition of Genghis Khan's descendants. Five years later, the dynasty was restored.

In 1470, Khan Batmönh unified Mongolia for 40 years. But his death led to greater fragmentation.

The 15th-17th centuries witnessed the birth of numerous legal documents drafted by Mongolian lords. During the empire, the great law Yasa alone governed society. So when each prince sought to become independent, they produced numerous laws and other binding documents. For example, Khan Altan's legal code was enforced in the Tumed region. "The Mongol-Oirad Law" and "The Religious Code" rank among the most important.

In 1575, the Manchus arrived and assailed the Ming Chinese dynasty. Their leader Nurhaci declared his kingdom Ching in 1616. The Manchu army invaded Mongolia and exerted pressure on Mongolian lords.

In 1636, the council of Inner Mongolian princes admitted defeat and recognized the authority of the Manchu emperor. The last of Genghis Khan's line, Khan Ligdan, resisted the Manchus until his death in 1634. This marked the end of a great dynasty. The situation worsened as some Mongols joined the Manchu army to share in their victories.

In 1691, the princes of Outer Mongolia decided to accept the domination of the Manchu Empire, leaving Zungaria as the only independent Mongolian province.