The spatial variability of soil nutrients can improve the yield per unit area of food crops and protect the agricultural ecological environment. Geostatistics and geographic information system (GIS) technology were applied to analyse the spatiotemporal variability and main influencing factors in soil organic matter (SOM) and soil total nitrogen (STN) in ecologically fragile regions of the Loess Plateau, China The results showed that the mean SOM and STN contents significantly increased in the past 40 years. Compared to the 1980 data, both SOM and STN global Moran's I indices are lower, with less spatial structure and an increased role for stochastic factors. The centre of gravity of soil nutrients in the study area mainly to the south-east, a reduction in the area of the ellipse and a tendency to concentrate the spatial distribution of nutrients. And it was concluded that the variation in nutrients was mainly influenced by fertiliser management practices. Therefore, a long time series of soil nutrient study is of great research value to clarify the soil nutrient status of the study area and to improve the efficiency of arable land use, as well as providing a theoretical basis for precision agriculture.