In the present study, 885 surface soil samples were collected to study the spatial variations and correlations between total contents of organic carbon (C), nitrogen (N) and sulfur (S) in surface soil across the Pearl River Delta (PRD) area. The results showed that soil C and N had similar spatial patterns, and the soil C:N ratio had a relative stable value of 9.63, suggesting that soil biological processes were the primary factor determining the soil C:N ratio. The spatial distribution of soil S was different from that of soil C and N, and there was no correlation between soil S and C. Soil samples with relatively high S content were mainly distributed along the regional rivers. The mean of soil C:S ratios was 42.6, and a constant C:S ratio did not exist. This finding revealed that the geochemical processes of soil S cycling and exogenous S inputs had more important effects on the spatial distribution of soil S, and soil C:S ratio than plant/microbe-related nutrient cycling. The present results revealed that soils with higher C and N content were more likely to accumulate C and N, while soils with lower C and N content could lose these nutrients more easily. Furthermore, the fertile farmland with high C and N content had excessive N input, while the poor farmland with low C content had an obvious N loss. The results demonstrated that the soil C:N ratio remained constant across the study area that is attributed to soil biological processes, whereas higher fluctuations were detected for the soil C:S ratio, which was primarily driven by geochemical processes and exogenous S inputs.