To solve the problem that indiscriminate subsidy policy is difficult to effectively exert an incentive effect on the investment behavior of enterprises, this paper puts forward a type of differentiated subsidy considering resource conditions, which consists of a basic security subsidy and a variable excitation subsidy. First, on the premise of guaranteeing the basic rate of return of enterprises, the net present value formula is used to compute the basic allowance. Then, according to the principal-agent theory, the revenue functions of government and enterprises are constructed, and the calculation model of the incentive scheme can be obtained by quantifying the correlation coefficients between resource conditions and social benefits. The case application shows that the Fuling block requires a significantly smaller amount of subsidy than the Weiyuan block due to its superior resources and development conditions, which verifies the necessity of considering regional differences in the design of shale gas development subsidies. This differentiated subsidy model can improve the efficiency of the use of financial funds while taking into account the fairness of policy implementation in different regions.