Excessive fertilizer application in the cropping industry leads to excessive nitrogen and phosphorus in surrounding water bodies, which causes farmers to increase economic cost and damage the environment. To address the problem, we built a crop-soil runoff soil column test system, setting eight fertilizer application levels for eggplants. Then, crop yield, soil fertility and pollutant concentrations in the receiving water bodies were measured. The process of fertilizer application on the water quality of surrounding receiving water bodies and the rationality of fertilizer application were analyzed. The results showed that crop yield, soil fertility, and pollutant concentrations in the receiving water increased with the increase in fertilizer application. The crop yield stabilized when the fertilizer application amount was higher than 0.12 kg/m2; the concentrations of total nitrogen (TN) and total phosphorus (TP) in the water increased significantly with the increase in fertilizer application, where particulate nitrogen (PN) and organic phosphorus (OP) were the key pollutants. In addition, crop growth had an interception effect on pollutant migration. The concentration of pollutants in the water was significantly lower in the late crop growth period (after flowering) than in the early. The crop had the best interception effect on pollutants when the fertilizer application was 0.12 kg/m2. The concentrations of TN and TP in the water were 29.7% and 22.3% after the flowering period, being lower than those before the flowering period. Therefore, a reasonable value of 0.12 kg/m2 is recommended for fertilizer application in this article. It can provide a reference for the fertilization system of eggplant planting in North China and theoretical support for the realization of clean production in small rural watershed planting.