Before 1644, the Manchu rulers pursued a deliberate policy of alliances with the southern (later “Inner”) Mongol tribes. In the 1630s the system of treaties and alliances gave way to the creation of the League-Banner system, the jasaq system, and the Lifan Yuan. The new territorial and political organization meant that the southern Mongols, while retaining a degree of autonomy, became subjects of the Qing dynasty. This essay explores the historical circumstances of the transformation of the relationship between Manchus and Mongols from partnership to subordination. It also aims to explain the political principles deployed by the Manchus in the redefinition of their relationship with the Mongol elites. More specifically, the essay proposes that the new forms of administration of Inner Mongolia stemmed from a condition of “tutelage.” Tutelage was not simply imposed by the Manchus upon their erstwhile allies, but actively sought by Mongol aristocrats in the context of the intra-Mongol wars carried out by the Čaqar leader Ligdan Khan.