The reconstruction of the spatial planning system in the new era should be based on the perspective of state governance, aim at realizing the modernization of the spatial governance system and governance capacity, and establish a spatial planning system following the guiding principles of the central government, community governance, and people-centered. Among them, straightening out the responsibility of the central and local governments and promoting the coordination are key to achieving the above objectives. Since the founding of the People’s Republic of China in 1949, the central-local government relationship during the evolution of China’s spatial planning system have gone through five stages: the planned economy period, after the decentralization reform, after the tax-sharing reform, the period of regulation under the concept of sustainable development, and the period of ecological civilization system reform. The development and reform of the spatial planning system at each stage is closely related to the evolution of the state governance system and the transformation of the centrallocal government relationship. In the new era, the central-local government relationship in China’s spatial planning system will present new synergy trends. The first one is equal rights and responsibilities: responsibility division of the central and local governments and market-oriented reform will be carried out simultaneously, and a clear institutionalized decentralization model will be established. The second one is that each department performs its duties: the central government stresses strategic guidance, bottom line control, and partial focus, and the local government focuses on elements allocation, quality improvement, and private rights coordination. The third one is collaborative and co-governance: spatial planning with regionelement coordination as the guidance and natural resource management as the support will become an important experimental field for improving the central-local government relationship.