Soil organic matter (SOM) scale effects are critical for crop growth and food security, especially in coal–grain complexes. However, few studies describe the spatial variation in SOM and its influencing factors at different sampling scales. Here, geostatistical theory and mathematical statistical methods were adopted to analyze the spatial variation characteristics of and structural differences in SOM in the coal mining subsidence area at Zhaogu No. 2 Mine at different sampling scales. The results showed that SOM varied spatially at large, medium, and small scales, and the coefficients of variation were 28.07%, 14.93%, and 14.31%, respectively, which are moderate values. The characteristic functions of the SOM content at different sampling scales differed, and the spatial structure scale effect was obvious. The spatial distribution of the SOM content fitted by the multiscale fitting model method was generally the same as the spatial distribution law of the SOM content fitted by the single scale kriging interpolation method; however, in terms of the detailed expression and spatial distribution of small-scale SOM content, the fitting model method was more accurate, and the accuracy increased by 36%. At the different sampling scales, sample size and soil type had specific effects on the SOM spatial distribution. These results provide research concepts and technical countermeasures for improving food security and the ecological environment in the coal–grain complex and help ensure sustainable agricultural lands.