The spatial variability of soil organic carbon (SOC) is scale- and location-dependent and controlled by various environmental factors. However, the location- and scale specific factors underpinning SOC variation often demand further investigation. This holds particularly true for topographically complex environments like China’s north-south transitional zone. In this paper, wavelet analysis was used to determine the relationship between SOC and environmental factors in the region. The results showed that SOC exhibits an obvious transition effect from north to south, especially at 140 km north of the transect. Elevation was the strongest single factor to explain SOC variations (percent area of significant coherence (PASC) = 25.20%, average wavelet coherence = 0.53 at all scales). Normalized difference vegetation index (NDVI), elevation, land surface temperature (LST) and topographic moisture index (TWI) were the strongest combination of factors explaining variation in SOC (PASC = 43.80%, average wavelet coherence = 0.94 at all scales). Edaphic factors, vegetative factors, climatic factors, topographic factors and their interactions jointly controlled the variation of SOC, and showed increasing predictive power at increasing spatial scales. Our results reveal the spatial sequence changes of SOC and the scale-location dependencies between SOC and environmental factors in China’s north-south transition zone, which can be used for modeling, mapping and management of SOC at different scales.