The phaeozem in Northeast China is rich in soil organic carbon (SOC). However, the excessive and inefficient application of chemical fertilizers, particularly nitrogen fertilizers, has primarily led to a decrease in soil pH in this region. Currently, the relationship between soil pH and the stability of soil organic carbon (SOC) remains ambiguous. This study, conducted over 13 years of field experiments, focused on soils exhibiting varying degrees of pH resulting from different nitrogen application rates. The research employed aggregate classification, ¹³C nuclear magnetic resonance spectroscopy, and analysis of microbial community composition to investigate the alterations in the SOC stabilization mechanisms under varying nitrogen application levels. Our results demonstrated that the decline in soil pH led to reductions in macroaggregates (>2 mm) and the soil aggregate destruction rate (PAD) by 4.8–14.6%, and in soil aggregate unstable agglomerate index (E_LT) by 9.7–13.4%. The mean weight diameter (MWD) and geometric mean diameter (GMD) exhibited significant declines (p < 0.05) with decreasing pH levels. According to the ¹³C NMR analysis, the SOC was predominantly composed of O-alkyl carbon and aromatic carbon. At a pH of 5.32, the Alip/Arom values decreased, while the molecular structure of SOC became more complex under different levels of pH. In addition, the increase in [Fe(Al)-OC] (31.4–71.9%) complex indicates a shift in the stability of organic carbon from physical protection to organic mineral binding. Declining soil pH significantly reduced the diversity of soil microbial communities and promoted a shift toward copiotrophic microbial groups. Overall, declining soil pH resulted in a decline in soil aggregate stability and an increase in SOC aromaticity. This drove the shift in the stabilization mechanism of SOC in the black soil ecosystem of meadows in Northeast China from physical protection to chemical stability.

Long-term intensive cultivation has degraded soil structure and reduced soil organic carbon (SOC) retention in the black soils of Northeast China. However, the processes underlying SOC accumulation under integrated soil–crop system management (ISSM) remain poorly understood. An 11-year field experiment compared farmers’ practice (FP), high-yield and high-efficiency practice (IP), super-high-yield practice (HY), and ISSM. We assessed SOC stocks, aggregate stability, organic carbon chemistry, extracellular enzyme activities, microbial carbon-use traits, microbial community composition, and microbial necromass carbon (MNC), and used partial least squares path modeling as an exploratory analysis of potential linkages. Compared with FP, ISSM increased SOC content and stock by 87.0 and 77.0%, respectively, and achieved an SOC sequestration rate of 2.8 Mg C ha⁻¹ yr⁻¹. ISSM also increased mean weight diameter and geometric mean diameter by 45.0 and 61.0%, increased microbial biomass carbon and carbon use efficiency by 205.2 and 100.0%, and decreased qCO₂ by 71.1%. Bacterial and fungal necromass carbon increased by 100.0 and 70.0%, respectively. The relative abundance of taxa operationally classified as growth-oriented also increased under ISSM. However, MNC/SOC did not differ significantly among treatments, while SOC aromaticity and hydrophobicity declined. Path analysis suggested that microbial carbon transformation was positively associated with necromass formation, whereas aggregate stability was associated with MNC and SOC retention. These results indicate that ISSM synchronously enlarged SOC and microbial necromass pools through sustained carbon inputs, efficient microbial transformation, and aggregate-mediated physical protection rather than through increased chemical recalcitrance.