Agricultural engineering plays a key role in agricultural and rural modernization. Innovation in agricultural engineering management should promote the prosperity of rural industry, promote the well-off life of farmers, and improve the level of ecological livability, and it is an important way to implement the strategy of rural revitalization. At present, agricultural engineering management system in China has not been effectively established, engineering management lags behind technology management, and the main roles do not fully act their functions. The management of agricultural engineering should be improved urgently, and the management efficiency should be improved urgently. In agricultural infrastructure engineering, agricultural mechanization engineering, protected agriculture engineering, agricultural products processing and storage engineering, agricultural products circulation engineering, resource and environmental protection engineering, agricultural information engineering and other major agricultural engineerings, management should be innovated by using the integrated methodology. The solution of a series of complex scientific problems in the agricultural engineering management needs the guidance of methodology, which is the integration and development of modern scientific methodology in agricultural engineering management. Focusing on the important demands of rural revitalization, the ‘four-all’ management system was proposed in this paper, which means the all-systems integration, all-factors integration, all-links optimization and all-department coordination in agricultural engineering. This system was used to analyze 3 key parts of agricultural engineering management which were target management, process management and dynamic control. In target management, various complex environmental factors, such as nature, society, humanity, technology and so on should be considered comprehensively. The overall objectives of agricultural engineering should be continuously controlled, coordinated and optimized. In the process management, considering the multi-department and multi-interest demands of the government, enterprises, scientific research institutions and farmers, emphasis should be placed on engineering practice, incentive and restraint mechanisms should be institutionalized in the whole process of agricultural planning, design, implementation, operation and retirement. In dynamic control, the external risks such as market risk, natural risk, technological risk, financial risk and engineering self risks should be faced, and feed forward control, field control and feedback control should be combined. Finally, specific suggestions on strengthening top-level design of agricultural engineering, division roles and coordination among departments, legislative construction, supervision and evaluation were put forward. This methodology system is expected to provide reference for agricultural engineering management.