The current assessment of the positive and negative benefits of agricultural water use lacks a depiction of the overall internal energy flow, which lead to the identification and analysis of agricultural water use benefits are not comprehensive enough. Based on the “water supply - water use and consumption - drainage - pollutant carrying” link in the ecological economic system of agricultural water resources, the energy conversion relationship of each link were analyzed, and the main connotation and composition of the positive and negative benefits of agricultural water use were raised, then a set of emergy quantitative method system of the positive and negative benefits of agricultural water use was built. Taking Zhengzhou city as an example, the positive and negative benefits of agricultural water use in 2017 were calculated. The research results show that the negative benefits of agricultural water resources eco-economic system production account for 37.93% of the positive benefits. The main reason for the negative benefits is non-point source pollution caused by TN, TP and COD.Consequently, developing production and social policies to limit the amount of non-point source pollution caused by pollutants in agricultural production is an effective way to increase the efficiency of agricultural water production while reducing the negative benefits generated.