In view of the particularity of the riparian zones in the Three Gorges Reservoir Region (TGRR), whether to protect, repair or harness it has become a realistic problem for policy makers. In this study, from the perspective of riparian zoning, the system construction scheme of riparian zones in the TGRR was put forward. It is necessary to balance and coordinate the objectives of the riparian zones. We systematically sorted out the alternative measures for protection, governance and restoration, such as ecological protection, ecological restoration and ecological governance measures. Finally, the divisional construction scheme of the riparian zones in the TGRR was proposed. The protection, restoration and management of the riparian zones need to be organically combined. The purpose is to conserve water and soil to the maximum extent, reduce various pollutants, maintain the ecological security, and ensure the water quality safe in the TGRR.