Abstract: To investigate the spatial patterns of soil organic matter (SOM) at the county scale in karst transition zones, this study focused on Xingwen County, Sichuan Province. Based on 3,497 surface soil samples, the study analyzed the characteristics of SOM, total nitrogen (TN), total phosphorus (TP), and pH. It revealed differences in SOM across different stratigraphic units and elevation ranges and estimated the density and reserves of surface soil organic carbon (SOC). The results indicate that the mean SOM content in the study area’s surface soil was 22.70 × 10⁻³; spatial variation was significant; the soil was slightly acidic (mean pH 5.71); TN was relatively abundant, while TP was relatively low. Geological background was the dominant factor controlling the spatial variation of SOM, with elevation serving as a secondary influencing factor. The Permian stratigraphic unit exhibited the highest mean SOM content (29.77 × 10⁻³), with the soil SOM content in the coal-bearing clastic rock area of the Yuanjiadong–Xingwen Formation reaching as high as 36.39 × 10⁻³. while the Jurassic strata had the lowest (16.80 ×10⁻³). Furthermore, SOM content in high-altitude areas (>1,000 m) was approximately 35% higher than in low-altitude areas (<400 m); Soil fertility exhibits a pattern characterized by “sufficient nitrogen, phosphorus deficiency, and relatively abundant organic matter”; the average surface soil carbon (SOC) density is 3,423 t/km², with a total stock of approximately 3.88 × 10⁶ t, and the soil carbon density in the Permian stratigraphic unit is about 1.77 times that of the Jurassic. These findings provide geochemical evidence to support geologically based zoning for farmland fertility improvement in karst transition zones, differentiated carbon sink management (strict protection of high-carbon-density Permian soil areas and carbon enrichment and fertility improvement in low-carbon-density Jurassic soil areas), and precise regulation of phosphorus nutrients.