In agricultural production, the main cause of groundwater pollution has been the leakage of total Nitrogen (TN) caused by excessive water and fertilizer application. In this study, an experiment combining a field and indoors was used to seek optimal coupling scheme and prevent groundwater pollution caused by excessive fertilization. Results showed that in recent years, groundwater quality has been deteriorating, and nitrate levels have increased by approximately three times (2014-2016). The TN accumulated significantly in a different soil layer, along with crop growth. The N accumulated mainly in the bottom of the studied soil layer (80-160 cm) over time. Under different water fertilizer treatments, the crop yield, leakage, and N use efficiency (NUE) were obviously various. The effect of irrigation water quantity was more significant for N leakage than fertilizer (P<0.05), and more water resulted in more N leakage. Additionally, considering the comprehensive benefits for winter wheat, medium fertilizer (N, 225 kg ha^-1) is an optimal scheme with medium water (3150 m³ ha^-1). For summer maize, medium water (1350 m³ ha^-1) and high fertilizer (N, 162 m³ ha^-1) were optimal treatment. The above schemes have the best comprehensive benefits for agricultural production in the case area.