Black soil is fertile, abundant with organic matter (OM) and is exceptional for farming. The black soil zone in northeast China is the third-largest black soil zone globally and produces a quarter of China’s commodity grain. However, the soil organic matter (SOM) in this zone is declining, and the quality of cultivated land is falling off rapidly due to overexploitation and unsustainable management practices. To help develop an integrated protection strategy for black soil, this study aimed to identify the primary factors contributing to SOM degradation. The geographic detector, which can detect both linear and nonlinear relationships and the interactions based on spatial heterogeneous patterns, was used to quantitatively analyze the natural and anthropogenic factors affecting SOM concentration in northeast China. In descending order, the nine factors affecting SOM are temperature, gross domestic product (GDP), elevation, population, soil type, precipitation, soil erosion, land use, and geomorphology. The influence of all factors is significant, and the interaction of any two factors enhances their impact. The SOM concentration decreases with increased temperature, population, soil erosion, elevation and terrain undulation. SOM rises with increased precipitation, initially decreases with increasing GDP but then increases, and varies by soil type and land use. Conclusions about detailed impacts are presented in this paper. For example, wind erosion has a more significant effect than water erosion, and irrigated land has a lower SOM content than dry land. Based on the study results, protection measures, including conservation tillage, farmland shelterbelts, cross-slope ridges, terraces, and rainfed farming are recommended. The conversion of high-quality farmland to non-farm uses should be prohibited.