Atmospheric nitrogen (N) deposition increases N availability in soils, with consequences affecting the decomposition of soil carbon (C). The impacts of increasing N availability on surface soil C dynamics are well studied. However, subsurface soils have been paid less attention although more than 50% soil C stock is present below this depth (below 20 cm). This study was designed to investigate the response of surface (0–20 cm) and subsurface (20–40 cm and 40–60 cm) C dynamics to 0 (0 kg N ha⁻¹), low (70 kg N ha⁻¹) and high (120 kg N ha⁻¹) levels of N enrichment. The soils were sampled from a cropland and a grass lawn and incubated at 25 °C and 60% water holding capacity for 45 days. Results showed that N enrichment significantly decreased soil C mineralization (Rs) in all the three soil layers in the two studied sites (p < 0.05). The mineralization per unit soil organic carbon (SOC) increased with profile depth in both soils, indicating the higher decomposability of soil C down the soil profile. Moreover, high N level exhibited stronger suppression effect on Rs than low N level. Rs was significantly and positively correlated with microbial biomass carbon explaining 80% of variation in Rs. Overall; these results suggest that N enrichment may increase C sequestration both in surface and subsurface layers, by reducing C loss through mineralization.