In the process of the Communist Party of China’s continuing historical struggle，“doing well in the pilot program is of great significance for the overall reform”. In order to better grasp and apply the methodology of the reform pilot program in the new era，an explanation framework for the system of China’s rural reform pilot areas is constructed to examine the sample cases of agricultural and rural policies and reform， which can explore the operational logic of China’s rural reform pilot program. Research has found that the rural reform pilot zone is a systematic field connecting the state and society. After receiving the “environmental pressure” from the central government’s intentional design and full process tracking， its internal focus is on the substantive operation of the “transmission system drive system”. Within discretionary space， it implements and expands experimental tasks， outputs innovative， integrated typical cases， and further transforms information through feedback loops， promoting local experiences to become national policies. As a result， we can conclude the operation logic of the pilot program in China’s continuous and in-depth rural reform： under the guidance of CPC， it is the strategic premise of comprehensively deepening reform to always stand at the top of the country for decision-making design； building a systematic and coordinated vertical organizational system is the endogenous fulcrum for comprehensively deepening reforms； knowledge production under the entral attention allocation is the core issue of comprehensively deepening reform；absorbing typical cases and radiating driving forces is the ultimate goal of comprehensively deepening reform. In this process， the pilot action of rural reform is moving towards a new normal of benign interaction between top-level design and practical exploration.