After entering into the 21st century, China's agricultural subsidy system has undergone adjustment and gradually realized the transformation of subsidy links, subsidy objects, and policy objectives and diversified policy tools. However, there are still problems such as poor adaptability to new problems, low legal level, poor policy effect and imbalance of rights and obligations. In order to solve the above problems, the agricultural subsidy system should be designed with the goal of realizing the adjustment mechanism of subsidy policy, ensuring the decisive role of market in resource allocation and improving the policy effect of agricultural subsidy, and on this basis, six mechanisms should be constructed. Finally, China should pay special attention to the combined application of various agricultural subsidy policy tools on the basis of abiding by WTO rules and combining with agricultural practice innovation support projects.