With the continuous advancement of rural industrialization and urbanization, the problems such as unclear property rights of rural collective assets and imperfect benefit distribution mechanism are becoming more and more prominent, so the reform of rural collective property rights system is imperative. Based on the practice of rural collective property rights reform in Nanjing, this paper summarizes the progress, effectiveness and experience of rural collective property rights reform. On this basis, it points out the problems existing in the current reform, such as simple allotment of shares by members, imperfect equity management, imperfect rights and powers of equity, slow progress of the separation of politics and economy of the village, and failure to fully release the reform dividend. It also analyzes the deep-seated causes of the problems, and finally puts forward the direction and supporting policies for deepening the reform.