In order to improve the management efficiency of water resource in China, and realize a reasonable collocation of irrigated water resources, the farmland water conservancy management is an important means to achieve the agricultural water saving and using. The research is based on the stochastic frontier production function to evaluate the management technique efficiency of water conservancy, and select the linear inefficient regression and Logistic model to explain the participatory mechanism which influences more obviously water management efficiency. The result shows that the management efficiency of water conservancy in China has yet to be improved to a large extent. The level of water management efficiency differs in different economic and natural regions as well as different management modes adopted. Increasing non-collective property, establishing water fee system and improving farmer's participation could contribute to the improvement of the efficient use of agricultural water resources. The research results can help different regions construct a suitable farmer's participatory mode and promote continuous use of agricultural water in China, which all have a great practical significance and reference value.