In the history of the religion-state relationship in China, a model of subordination of religion to the state has been dominant for centuries. In recent years, some Chinese Protestant churches have advocated the model of separation of church and state. Through a historical and theological analysis, this study argues that in order to relieve the tensions between Chinese Protestantism and the contemporary Chinese government, a better conceptual alternative is to reconsider the issue in terms of autonomy rather than separation or subordination, and to argue for legally allowing the coexistence of both official and nonofficial churches and grant different degrees of autonomy to each.