In order to comprehensively and objectively understand the characteristics of spatial and temporal differentiation of utilization efficiency of agricultural green water resources in China, promote the water ecological civilization construction and utilization of agricultural green water resources, this paper uses SE-SBM model considering undesirable outputs to calculate the utilization efficiency of agricultural green water resources of 31 provinces in China from 2002 to 2020, taking agricultural non-point source pollution level as the undesirable output. The ML index, Theil index and “efficiency-productivity” matrix were introduced to analyze the spatial and temporal differentiation of utilization efficiency of water resources. The results show that the utilization efficiency of agricultural green water resources in 26 provinces fluctuates steadily, and the order is Eastern > Northeastern> Central> Western regions. Intertemporal dynamic development has its own advantages and disadvantages. The ML index first decreased and then increased, EC and TC accounting for 73.68% of the study period show the “trade-off”. About 62.11% of the overall gap in utilization efficiency of water resources come from the intra-regional gap mainly consist of western region, but the inter-regional gap can’t be ignored.