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Soil erosion along with soil particles and nutrients losses is detrimental to crop production. We carried out a 5-year (2010 to 2014) study to characterize the soil erosion and nitrogen and phosphorus losses caused by rainfall under different fertilizer application levels in order to provide a theoretical evidence for the agricultural production and coordinate land management to improve ecological environment. The experiment took place under rotation cropping, winter wheat-summer maize, on a 15° slope purple soil in Chongqing (China) within the Three Gorges Region (TGR). Four treatments, control (CK) without fertilizer, combined manure with chemical fertilizer (T1), chemical fertilization (T2), and chemical fertilizer with increasing fertilization (T3), were designed on experimental runoff plots for a long-term observation aiming to study their effects on soil erosion and nutrients losses. The results showed that fertilization reduced surface runoff and nutrient losses as compared to CK. T1, T2, and T3, compared to CK, reduced runoff volume by 35.7, 29.6, and 16.8 %, respectively and sediment yield by 40.5, 20.9, and 49.6 %, respectively. Regression analysis results indicated that there were significant relationships between soil loss and runoff volume in all treatments. The combined manure with chemical fertilizer (T1) treatment highly reduced total nitrogen and total phosphorus losses by 41.2 and 33.33 %, respectively as compared with CK. Through this 5-year experiment, we can conclude that, on the sloping purple soil, the combined application of manure with fertilizer is beneficial for controlling runoff sediments losses and preventing soil erosion.