Soil organic matter (SOM) is an important carbon pool in terrestrial ecosystems and plays a key role in soil functions. Nevertheless, the effects of fertilization practices on the physical, chemical, biological, and comprehensive stability of SOM are still unclear. We carried out a long-term field experiment in the northeast black soil region in China with four different fertilization practices: no fertilizer (CK), single chemical fertilizer (NPK), chemical fertilizer + straw (NPKJ), and chemical fertilizer + organic manure (NPKM). The content of particulate organic matter (POM) and mineral-associated organic matter (MAOM), compound composition of SOM, carbon mineralization characteristics, active soil organic matter (ASOM), and inert soil organic matter (ISOM) were tested. The results showed that the application of fertilizers significantly increased the contents of POM and MAOM to 2.59–4.65 g kg⁻¹ and 32.69–34.65 g kg⁻¹ (p < 0.05), but decreased the MAOM/POM values by 37.8–42.4%, indicating reduced the physical stability of SOM. Fertilization practices increased the contents of aromatic, nitrogen-containing compounds and decreased the oxygen compounds of SOM, representing enhancement of the chemical stability. The contents of ASOM and ISOM increased in fertilization practices, while the biological stability index (BSI) under the NPKJ and NPKM treatments was lower than the CK treatment, suggesting that the biological stability decreased under the manure and straw application. In addition, the comprehensive stability of SOM increased by 26–116% through a reduction in the physical and biological stability, coupled with an increase in the chemical stability. Collectively, our study demonstrated that the application of manure and straw enhanced both the comprehensive stability and content of SOM and reduced the physical and biological stabilities while increasing the chemical stability, which made the largest contribution to the comprehensive stability.