Within an orchard containing 12-year-old late-maturing peach trees (cultivar “Hujing”) in Taihu Lake Basin, China, different fertilizer application rates and management practices were applied to explore the technological approaches to coordinate the high quality and high yield of peach during 2012—2013. The effects of these treatments on soil nitrogen loss by surface runoff in the typical peach orchard were investigated under natural rainfall conditions. In T1 (conventional fertilization practice), total nitrogen concentration (TN)in the surface runoff water reached the peak value of 87.72 mg/L, and TN showed a decreasing trend with the peach growth period. Compared with T1, T2 (reducing fertilization practice to 70% of conventional) and T3 (Inter-planting white clover (Trifolium repens L.)) significantly reduced the average TN in whole peach growth period, which decresed by 26.16% and 12.89%, respectively. In T1, the quantity and coefficient of TN losses by surface runoff reached up to 52.06 kg/hm2 and 6.21%, respectively; these mainly occurred from the peach fruit setting stage to the peach fruit ripening stage, and the strong typhoon season after peach fruit harvest. Compared with T1, T3 significantly reduced the quantity and coefficient of TN losses by 7.41% and 7.41%, respectively. T2 significantly reduced the quantity of TN losses by 26.96%, but TN loss coefficient slightly increased by 3.99%. However, compared with T1, T3 and T2 significantly reduced the partial coefficient of TN losses by surface runoff by 9.51% and 20.70%, respectively.