Chinese Loess Plateau is considered as one of the most serious soil loss regions in the world, its annual sediment output accounts for 90 % of the total sediment loads of the Yellow River, and most of the Loess Plateau has a very typical characteristic of "soil and water flow together", and water flow in this area performs with a high sand content. Serious soil loss results in nitrogen and phosphorus loss of soil. Special processes of water and soil in the Loess Plateau lead to the loss mechanisms of water, sediment, nitrogen, and phosphorus are different from each other, which are greatly different from other areas of China. In this study, the modified export coefficient method considering the rainfall erosivity factor was proposed to simulate and evaluate non-point source (NPS) nitrogen and phosphorus loss load caused by soil and water loss in the Yanhe River basin of the hilly and gully area, Loess Plateau. The results indicate that (1) compared with the traditional export coefficient method, annual differences of NPS total nitrogen (TN) and total phosphorus (TP) load after considering the rainfall erosivity factor are obvious; it is more in line with the general law of NPS pollution formation in a watershed, and it can reflect the annual variability of NPS pollution more accurately. (2) Under the traditional and modified conditions, annual changes of NPS TN and TP load in four counties (districts) took on the similar trends from 1999 to 2008; the load emission intensity not only is closely related to rainfall intensity but also to the regional distribution of land use and other pollution sources. (3) The output structure, source composition, and contribution rate of NPS pollution load under the modified method are basically the same with the traditional method. The average output structure of TN from land use and rural life is about 66.5 and 17.1 %, the TP is about 53.8 and 32.7 %; the maximum source composition of TN (59 %) is farmland; the maximum source composition of TP (38.1 %) is rural life; the maximum contribution rates of TN and TP in Baota district are 36.26 and 39.26 %, respectively. Results may provide data support for NPS pollution prevention and control in the loess hilly and gully region and also provide scientific reference for the protection of ecological environment of the Loess Plateau in northern Shaanxi.