Nitrogen (N) and phosphorus (P) losses from agroecosystems are dominant nonpoint pollution. To minimize the losses of N and P, the optimal depth of fertilization was explored using a soil column study with the red paddy soil as the research objects. The losses of N and P were measured under five depths of fertilization (0, 5, 7.5, 10, and 12.5 cm) as well as no fertilization. The results showed that ammonia volatilization was significantly decreased with increasing fertilization depth within 0–10 cm, and there was no significant difference among the 10 cm, 12.5 cm, and no-fertilization treatments. Comparing with surface fertilization (0 cm), N and P losses by runoff could be reduced by 30.7–67.1% and 96.9–98.7% respectively by fertilization at 5–12.5 cm. In addition, deep fertilization (5–12.5 cm) did not increase N and P losses by leaching at the depth of 40 cm. Total N and P contents in the tillage layer of soil were increased by 5.1 to 22.8% and by −1.0 to 7.5%, respectively. Fertilization at 10cm depth has the potential to minimal environmental impact in the red paddy soil of south China, at this depth, NH3 volatilization was reduced by 95.1%, and N and P losses by runoff were reduced by 62.0% and 98.4%, respectively, compared with surface fertilization.