Purpose Soil organic carbon (SOC) is an important parameter determining soil fertility and sustaining soil health. How C, N, and P contents and their stoichiometric ratios (C/N/P) regulate the nutrient availability, and SOC stabilization mechanisms have not been comprehensively explored, especially in response to long-term fertilization. The present study aimed to determine how the long-term mineral and manure fertilization influenced soil C/N/P ratios and various protection mechanisms underlying the stabilization of OC along with profile in a cropland soil. Materials and methods The soil was sampled from five depths, viz., 0-20 cm, 20-40 cm, 40-60 cm, 60-80 cm, and 80-100 cm, from plots comprising wheat-maize-soybean rotation system subjected to the long-term (35 years) manure and mineral fertilizer applications. Results and discussion Results revealed that the soil C, N, P stoichiometry and their contents in topsoil depths (0-20 and 20-40 cm) and subsoil depths (40-60, 60-80, and 80-100 cm) varied significantly (p < 0.01) among the soil layers. Compared with CK, the C, N, and P contents were significantly higher (p < 0.05) in NPKM in the topsoil layers, while M alone increased these contents throughout the subsoil. Overall, the C, N, and P contents and their stoichiometry decreased with the increase in depth. Regression analysis showed that C/N, C/P, and N/P ratios associated significantly with the OC fractions in the topsoil layers only. These negative correlations indicated that these ratios significantly influence the C stabilization in the surface layers. However, the results warrant further investigations to study the relationship between soil and microbial stoichiometry and SOC at various depths. Conclusions Long-term manure applications improved the C sequestration not only in the topsoil but also in the deep layers; hence, these facts can be considered relevant for fertilizer recommendations in cropping systems across China.