Based on analysis of the input and output of various ecological flows in a regional agricultural production system, the positive and negative effects of agricultural water utilization were evaluated through emergy analysis from a perspective of ecological economics. Then, with the emergy as a normalized basis, the method of calculating the positive and negative effects of agriculture water utilization was improved. Using Zhengzhou City as an example, the positive and negative effects of water utilization in the agricultural production system of the city in 2011 were calculated. The results show that the positive effect was 1.62 × 10²¹ J, and the negative effect was 6.82 × 10²⁰ J, which was about 42.10% of the positive effect, indicating that the city's agriculture water utilization was in a significantly negative situation. Improving the utilization efficiency of water resources and the accompanying renewable resources while minimizing the unreasonable investment and utilization of nonrenewable resources, and avoiding the harm caused by environmental pollution and overexploitation of groundwater are the keys to solving the problem of negative effects of agricultural water utilization.