The ‘Grain-for-Green’ program implemented on the Loess Plateau in China has dramatically changed land use types, and subsequently enhanced the spatiotemporal variability of soil organic carbon (SOC) in the watersheds. However, the spatiotemporal variability of SOC for different topographic and land use types within small watersheds has not been adequately explored following the implementation of the ‘Grain-for-Green’ program. In this study, we determined the spatiotemporal variability of SOC content using the data collected in 1993, 2002, 2005, and 2012 and measured in 2018 and identified its driving factors for different topographic (tableland, sloping land, and gully) and land use types in the Wangdonggou watershed on the Loess Plateau. The spatial patterns of SOC content differed among tableland, sloping land, and gully, with higher spatial variability in gully than sloping land and tableland. The SOC content in the 0–20 cm soil layer in 2018 increased by 8.58%, 26.4%, and 22.2%, compared to 2002, for tableland, sloping land, and gully, respectively. Woodland and grassland had a great potential to sequester and stabilise carbon. The vegetation cover was a relatively dominant factor affecting SOC content throughout the watershed. Our results indicate a close relationship between SOC content and topographic, vegetation, and edaphic variables. This information is critical for understanding SOC dynamics at the watershed scale for sustainable ecological restoration.