Aiming at the problem of responsibility transfer and management imbalance in watershed management caused by the flow characteristics of floating debris, a “government-enterprise” synergistic governance model based on evolutionary game theory is constructed from the perspective of the function transformation of the central government. Taking the Three Gorges Reservoir area as an example, this study performs a simulation analysis to reveal how regulatory mechanisms and critical factors influence the effectiveness of synergistic governance in managing floating debris within the reservoir area. The results show that the central government’s comprehensive implementation of reward and punishment policies and adjustment mechanisms can make the system quickly reach a synergistic governance equilibrium. However, its supervision shows a diminishing marginal utility. Compared with the mainstream cooperation between the government and enterprises, the local government’s implementation of tributary source control will have a more evident positive effect on the strategic choice of project owners. When the project owner increases the positive governance subsidy and reduces the negative governance subsidy, the interest difference between the two strategies will become more significant for the local government, and it will be more inclined to choose the positive governance strategy. Therefore, the differentiated subsidy strategy is the driving force of “government-enterprise” synergistic governance.