In the process of the ecological civilization construction, the hierarchical administrative responsibility system, which is typical of river chief system, has become the most important way, and has been implemented in other fields of natural resources, showing a characteristic of “simplified governance”. From the perspective of natural resources property rights, this paper compares the implementation of river chief system and the forest chief system, and then suggests that because of the difference in the property rights structure, different natural resources tend to differ in the governance mechanism. Therefore, the simplified governance can lead to the phenomenon of “empty system”. On this basis, this paper proposes the implementation of a multiple governance mechanism of combined state, market, and community.