Nitrogen deposition is a global environmental problem that can alter soil organic carbon (SOC) storage. However, the magnitude and depth-dependent response of SOC to nitrogen deposition remain unclear. Here, we conducted a meta-analysis of 113 paired observations from 57 publications to quantify the effects of nitrogen deposition on SOC stocks in different soil layers (0–10, 10–20, 20–30, 30–50, and 50–100 cm). We found that nitrogen deposition significantly increased SOC stocks in the 0–10 and 10–20 cm soil layers by 13.5% and 12.8%, respectively, but decreased SOC stocks in the 30–50 cm soil layer by 11.1%. The positive effects of nitrogen deposition on SOC stocks in the upper soil layers were mainly driven by increased plant productivity and litter inputs, while the negative effect in the 30–50 cm soil layer might be attributed to the accelerated decomposition of SOC. Our results suggest that nitrogen deposition can have complex and depth-dependent effects on SOC storage, which should be considered in terrestrial carbon cycle models and ecosystem management.