Understanding the spatiotemporal distribution of soil organic carbon (SOC) and its controlling factors is extremely important for improving soil quality and developing sustainable management practices. We quantified spatiotemporal variations in SOC in three typical regions (Shuyang, Rugao, and Shanghai) in southeastern China during 1981–2011, by using geographically weighted regression (GWR), and explored the drivers with a geographical detector method. A total of 219 topsoil samples were collected in the three regions to measure the SOC in 2011, and a total of 109 SOC data for 1981 were obtained from the soil survey reports of Shuyang, Rugao, and Shanghai, which involved in the database of the second national soil survey of China. The results showed that the mean SOC contents in 2011 were 14.68 g kg⁻¹, 9.55 g kg⁻¹, and 18.00 g kg⁻¹ in Shuyang, Rugao, and Shanghai, respectively. The topography (q = 0.60) and the sand content of the soil (q = 0.70) were the main drivers of the spatial variability in the SOC in Shuyang and Rugao, while the carbon inputs (q = 0.68) predominantly explained the spatial heterogeneity of the SOC in Shanghai. Significant increases in SOC storage occurred in Shuyang and Rugao from 1981 to 2011, with increase rates of 0.55 t ha⁻¹ yr⁻¹ and 0.26 t ha⁻¹ yr⁻¹, respectively. Land use change (dryland farming to rice cultivation) was identified as the largest driver of the SOC increases in Shuyang and Rugao (q values of 0.16 and 0.09, respectively), followed by increasing carbon inputs (0.14 and 0.07). However, the SOC storage in Shanghai rapidly decreased at a rate of −0.38 t ha⁻¹ yr⁻¹ during 1981–2011. The land use change from wetlands to rice cultivation was the primary reason for the decreasing SOC (q = 0.24), and a net decrease in carbon inputs between 1981 and 2011 was another main driver of the reduction in the SOC in Shanghai (q = 0.14). Our results from this study provide important information on the spatiotemporal changes in SOC and its drivers to the scientific community and decision-makers, for the development of management strategies to sustain soil fertility in many areas with rapid economic development and increasing populations.