Soil organic carbon (SOC) content is one of the most important indicators of soil sustainability. Understanding how soil and water conservation (SWC) measures affect the SOC stock is important for the protection of soil and water quality. In the present study, the impacts of SWC measures on the SOC stock change in a typical small watershed in the Mollisol region of Northeast China were investigated using a grid soil sampling scheme. A total of 292 soil samples were collected in the same locations in 2005 and 2016. The results indicated that the average annual increase rate of SOC was 5.43%. The equivalent soil mass (ESM) method indicated that the change rate of the SOC stock significantly increased from 2005 to 2016, with an average annual increase rate of 3.33%. The SOC stock change was significantly affected by the SWC measures, the initial SOC content, and the interaction between the SWC measures and the initial SOC content. Furthermore, grassland had a greater change rate of the SOC stock than the other SWC measures (P < 0.05). As the initial SOC content increased, the change rate of the SOC stock significantly decreased (P < 0.05). The change rate of the SOC stock in forestland significantly increased with an increase in the initial SOC level, but the opposite trend was found in the grassland and terrace (P < 0.05). In addition, soil erosion occurred on the upper and middle slopes, and soil deposition occurred on the foot slope in the typical sloping farmland (P < 0.05); forestland had better control effect on soil erosion than farmland. Our findings provide science-based recommendations for enhancing SOC storage in agricultural sites by implementing SWC measures.