China’s decades of late supporting policies for reservoir resettlement have played an important role in the restoration of resettlers’ livelihood and shared development, but also produced many unexpected consequences in practice. Under the background of county integration and common prosperity, it has both theoretical and practical significance to systematically sort out the practice forms and deep-seated reasons of the unintended consequences and build the transformation framework and realization path of the late supporting policies. This paper illustrates the unintended consequences of reservoir resettlement supporting policies from a multidisciplinary perspective. It is found that the practice forms mainly include: the unscientific verification method of resettlers status leads to a surge in the number of resettlers, the resettler status inhibits the social integration of the resettlement areas, the continuous national supporting induces the risk of moral crisis for resettlers, the continuous supporting causes double deprivation to the aborigines, the local resettlement agencies, based on departmentalism, hope that the resettlers will exist for a long time, and the top-level designers face a dilemma when formulating the late resettlement supporting policy. Combined with the development strategy of China in the new era and new situation, based on the trinity theoretical framework of support subjects, support methods and support resources, this paper puts forward the transformation path of the late resettlement supporting policy in order to provide policy suggestions for the formulation of the late resettlement supporting policy in the next stage. At the same time, the good practice and system design of the late support for reservoir resettlement can also provide useful reference for the late support of relocation being implemented in China.