Long-term organic inputs increase soil organic carbon (SOC) in black soil; however, it remains uncertain if straw and manure enhance SOC via separate microbial necromass carbon (MNC) routes. Therefore, a 12-year field experiment was conducted to explore this mechanism. Treatments included inorganic fertilizer, partial substitution of inorganic fertilizer with straw, and partial substitution of inorganic fertilizer with manure, along with a no-fertilizer control. According to the results, compared with inorganic fertilizer alone, treatments involving both organic manure and straw returned markedly raised the levels of SOC, MNC, bacterial necromass carbon (BNC), and fungal necromass carbon (FNC). Notably, compared to the CK treatment, N75S showed a greater contribution of MNC to SOC (MNC/SOC), but in both N75M and M, the MNC/SOC was lower than in CK. The CAZyme genes related to hemicellulose, lignin, chitin, and peptidoglycan differed among treatments. Elevated gene abundances for plant-derived lignin and hemicellulose decomposition were observed under M and N75M, whereas they reduced the genes responsible for peptidoglycan and glucan. However, under N75S, there was a notable rise in the number of genes responsible for hemicellulose and lignin, as well as an increase in genes that degrade chitin and peptidoglycans. In conclusion, this finding demonstrates that long-term straw return tends to promote SOC stabilization primarily through the microbial necromass pathway, while the application of manure over the long term tends to increase the total SOC primarily through the input of exogenous organic carbon.