Recommended nitrogen fertilization enhances soil carbon sequestration in China’s monsoonal temperate zone

China consumes more than one-third of the world’s nitrogen (N) fertilizer, and an increasing amount of N fertilizer has been applied over the past decades. Although N fertilization can increase the carbon sequestration potentials of cropland in China, the quantitative effects of different N fertilizer application levels on soil carbon changes have not been evaluated. Therefore, a 12-year cultivation experiment was conducted under three N fertilizer application levels (no N fertilizer input, the recommended N fertilizer input after soil testing, and the estimated additional fertilizer input) to estimate the effect of N addition on soil carbon changes in the root layer (0–80 cm) and non-root layer (80–200 cm) using a within-study meta-analysis method. The results showed significant declines in the soil inorganic carbon (SIC) in the root layers and significant growth in the SIC in the non-root layers under N fertilizer input. The soil organic carbon (SOC) in the root layers and the non-root layer significantly decreased under all the treatments. In addition, the recommended N fertilizer application level significantly increased the SOC and soil total carbon stocks compared with the future N fertilizer application level and no N input, while the future N fertilization significantly decreased the SIC and soil total carbon compared with no N input. The results suggest that N fertilization can rearrange the soil carbon distribution over the entire soil profile, and the recommended N fertilization rather than excess N input can increase the soil carbon stock, which suggests that the national soil testing program in China can improve the soil carbon sequestration potential.