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Urban regeneration and rural revitalization are becoming major policy initiatives in China, which requires new approaches for sustainability transitions. This paper reviewed the history of policy reforms and institutional changes and analysed the main challenges to sustainability transitions in China. The urban-rural systems were defined as a complex dynamic social-ecological system based on resilience thinking and transition theory. The notions of adaptation and transformation were applied to compose a framework to coordinate “resilience” with “sustainability”. The findings indicate that China’s urbanization has experienced the conservative development of restructuring socio-economic and political systems (before 1984), the fast industrialization and economic development leaned to cities (1984 to 2002), the rapid urbanization led by land expropriation and investment expansion (2002 to 2012), and the quality development transformation equally in urban and rural areas (since 2012). The sustainability transitions have been challenged by controversial institutional arrangements, concerning population mobility control, unequal social welfare, and incomplete property rights. A series of policy interventions should be designed and implemented accordingly with joint efforts of multiple stakeholders and based on the combined technocratic and bottom-up knowledge derived from proactive and conscious individuals and collectives through context-dependent social networks.