In view of the negative ecological civilization problems brought about by economic development, such as the reduction of water source forest area, serious soil erosion, resettlement, and serious water pollution during the development of the Xijiang River Basin, this paper uses the evolutionary game method to explore the strategy and equilibrium of governance of the Xijiang River Basin between the Guangxi government and the Guangdong government. The research results show that under traditional circumstances, the game system of the two governments will evolve towards an inferior stable state (over-exploitation, unreasonable acceleration), which is not conducive to the green and sustainable development of the ecology of the Xijiang River Basin; There are 9 evolutionary scenarios in the game system when punished by “development” and “unreasonable acceleration” by the Guangdong government. If and only when specific conditions are met, the system will converge to the Pareto optimal state of (moderate development, reasonable acceleration); According to the penalty value, 9 different scenarios are designed to analyze the game results of the penalty value pair. Numerical simulations show that when the central government and the higher-level relevant departments give higher accountability and punishment to the two governments, the game system will move towards the Pareto optimal state; Therefore, in order to promote the balanced development of eco-economic development and governance in the Xijiang River Basin, in the design of the accountability mechanism, it is necessary to give the two governments a higher penalty value that meets the corresponding conditions.