The prohibition of aquaculture is an important policy instrument for water quality protection. However, there are lack of observations on the complex interactions between stakeholders in the limiting or closing of fisheries and the internal cooperative mechanism that balances the restoration of water bodies and the livelihoods of fishermen. Using evolutionary game theory and modeling, this article analyzes the complex mutual feedback strategy between local government and the affected fishermen in regard to water body restoration and livelihood security under fishing prohibition. The results show that (a) the performance evaluation mechanism of environmental protection, including rewards and punishments, can provide direct political traction and indirect material guarantees for local governments to perform their duties and allow water body restoration and the transition of fishermen to alternative livelihoods. (b) Whether the local government actively promotes aquaculture closures is restricted by the improvement in the aquatic environment, the aquaculture development under the existing livelihood, and the industrial economic benefits of the new livelihood. And the capacity of them contribute to the overall development of the local government. The development of the net income of both parties in the negotiation will shape the direction of a series of public policies that focus on aquaculture closures.