Studying the spatial variability and its affecting factors of surface soil organic matter and total nutrients can provide reference for soil management in the ecological fragile zone of the Loess Plateau. Based on the 93 soil sampling points in Wangdonggou watershed, this paper used a variety of geostatistical methods to analyze the spatial variability and its influencing factors of soil nutrients in the gully region of the Loess Plateau. The results showed that soil nutrient contents in the study area were at a moderate level. The spatial variability was in the following order: Total phosphorus > total nitrogen > organic matter > total potassium, and they were dominated by structural factors. Compared with total phosphorus and total potassium, organic matter and total nitrogen had smaller variation scale, weaker spatial autocorrelation and higher spatial complexity. Soil organic matter and total nitrogen presented a distribution pattern of high in the south and low in the north, and their main influencing factors included elevation, slope, curvature and land use. Total phosphorus was opposite to the former two, namely high in the north and low in the south. Elevation, slope, land use, soil mechanical composition and human activity had great influence on it. Total potassium was high in the center and low in the periphery, and its distribution was relatively scattered, and aspect and soil mechanical composition had a stronger effect on it. In view of the above results, regression prediction models between nine environmental factors and soil nutrients were established to provide data support for the sustainable use of soil resources in the study area.