This paper discusses the features and objectives of rehabilitated ecological compensation, uses bounded rationality evolution gambling model to analyze the evolutional stability strategy and dynamic tendency of water sources and water use areas, and applies Jacobian matrix to study anti-disturbance stability at each equilibrium points, aiming at offering references for China to develop ecological compensation mechanism of water sources. Upper-level governmental involvement in ecological rehabilitation and bilateral compensation constraint may make “rehabilitation in water sources and compensation in water use areas” the only balanced strategy if punishment and compensation meet some requirements, a premier balanced strategy expected publicly. This paper presents suggestions on increasing public consciousness in environmental protection, improving the laws and regulations, setting up cooperative platforms, and clarifying interests and responsibilities, which will help sound development of ecological compensation.