Soil organic carbon (SOC) and nitrogen (N) mineralization are important biogeochemical processes associated with soil fertility. These processes are influenced by physically, chemically, and biologically stabilized organic carbon (C) fractions, the mechanisms of which are not well-known. The present study was conducted to evaluate the combined effect of manure and mineral fertilizers on the content of C fractions to promote the mineralization of SOC and N. Treatments included: i) unfertilized control (CK), ii) a combination of nitrogen, phosphorus, and potassium (NPK), iii) manure (M), iv) manure combined with NPK (MNPK), and v) a high dose of manure combined with NPK (hMNPK). The combined use of manure and mineral fertilizers enhanced accumulation of the unprotected C fraction (cPOC) by 44-72% compared to the CK. Manure application enhanced physical (µagg), physico-chemical (H-µsilt), and physico-biochemical C (NH-µsilt) fractions by 30-56%, 62-150%, and 27-51%, respectively. In contrast, chemically and biochemically protected fractions showed a minor response to manure application. Accumulation of cPOC, C in microaggregates (µagg), and physico-chemically protected C fractions (H-µsilt and H-µclay) significantly contributed to the mineralization of SOC and N, resulting in a significant increase in rice grain yield with long-term manure additions. In summary, long-term use of manure and mineral fertilizers improved soil C accumulation in unprotected and physically protected fractions, which enhanced SOC and N mineralization and benefited soil productivity in a rice-wheat cropping system.