Evidence for the variability of the carbon (C) management index (CMI) across surface and subsurface soil layers due to long-term fertilization in diverse agroecological settings is inadequate. Thus, our study aimed to explore the variations in soil organic C (SOC), CMI, and its response ratio (RR-CMI) along soil profiles (0–60 cm) across four croplands in China. These croplands represented two high-fertility sites in Gongzhuling (GZL) and Chongqing (CQ) and two low-fertility sites in Zhengzhou (ZZ) and Qiyang (QY). We evaluated various treatments: control (CK; no fertilizer), inorganic fertilizer (NPK), NPK combined with standard manure (MNPK), and 1.5 times the standard rate of manure and NPK (1.5MNPK). The results indicated a significant increase in SOC content across all depths, ranking as 1.5MNPK > MNPK > NPK > CK, with ranking for the pattern observed across sites as GZL > CQ ≈ QY > ZZ. This led to the most substantial increases, reaching 107, 86, 105, and 62 % more than CK across the soil profile (0–60 cm) under 1.5MNPK across all sites. Moreover, the same treatment showed a significantly higher CMI at 0–60 cm compared to CK, with increases of 37, 19, 65, and 25 % for ZZ, QY, GZL, and QY, respectively. Notably, for the low-fertility soils (ZZ and QY), a higher CMI was observed in the 0–20-cm soil layer), whereas the opposite was true for the high-fertility soil (GZL). Consequently, low-fertility soils exhibited a higher RR-CMI in the 0–20-cm soil layer, whereas the high fertility site (GZL) showed a higher RR-CMI in the 40–60-cm soil layer, suggesting differential accumulation and loss of SOC regulated by soil depth and inherent site fertility. Partial least squares regression analysis further indicated that soil and climatic factors predominantly influenced CMI under long-term fertilization in typical Chinese soils. In conclusion, the long-term application of manure combined with inorganic fertilizer promotes SOC sequestration and enhances CMI, presenting a viable management strategy for enhancing soil quality in the studied regions.