Abstract: Reasonable compensation standard is the core of watershed ecological compensation, and it is also the key content of stimulating the enthusiasm of ecosystem service providers, reflecting the value of ecosystem service improvement and realizing regional coordinated development. Based on the cost-benefit perspective and taking Wei River Basin as an example, this paper calculates the cost-benefit of ecosystem service protection by using the full-cost method and choice experiment respectively, and then calculates the ecological compensation standard by using Rubinstein bargaining model. The results show that: (1) in order to improve the ecological condition of the river basin, the direct cost of Gansu Province in the upper reaches is about 350.212 7 million yuan /year, the indirect cost is about 1 071.122 6 million yuan /year, and the full cost is about 1 421.335 3 million yuan /year; (2) the benefits of improving the ecosystem services in the river basin can be 2 529.129 6 million yuan for Shaanxi Province in the middle and lower reaches; (3) on the premise of cost-benefit of ecosystem service protection, if upstream area has complete patience or downstream area has no patience at all, upstream area will get all net income, and the compensation standard is 2 529.129 6 million yuan /year; if upstream area is completely impatient and the patient level (discount factor) of middle and downstream area is 0.5, both sides will share the net income equally, that is, the compensation standard is 1 975.232 5 million yuan /year. Generally speaking, this study provides a feasible idea for cost-benefit analysis of ecosystem services protection and transboundary ecological compensation standard accounting. In practical application, discount factors can be reasonably set for both sides of the bargaining process according to specific conditions.