Vegetation succession triggers a non‐linear trajectory of <scp>SOC</scp> molecular architecture driven by microbial resource acquisition strategies

Abstract The molecular architecture of soil organic carbon (SOC) mediates long‐term persistence by regulating chemical diversity; however, how vegetation succession reshapes it via microbial functionality remains unknown. We integrated pyrolysis‐GC/MS, metagenomics and path analysis across a subalpine chronosequence (grasslands → shrublands → broadleaf → coniferous → primary forests) to resolve linkages among above‐ground vegetation, microbial‐mediated multifunctionality (MF) and SOC molecular diversity and network complexity. Results revealed a ‘decline‐then‐rise’ trajectory for SOC molecular diversity and network complexity. In the shrubland‐broadleaf stages, upregulated microbial degradation genes (starch/cellulose/hemicellulose/lignin) and high metabolic activity accelerated labile compounds decomposition (lipids decreased from 65.0% to 42.5%), causing a diversity minimum. Conversely, in coniferous stages (Sec. 4–6), molecular network complexity recovered due to SOC pool re‐diversification, characterized by a resurgence of lipids (from 29.1% in Sec. 3–4 to 42.3% in Sec. 6) and polysaccharides (from 3.3% in Sec. 4 to 11.9% in Sec. 6). Microbial‐mediated MF, representing resource acquisition intensity, was a pivotal integrative driver of SOC molecular architecture. MF dominated SOC signatures both directly (path coefficient = −0.50, p &lt; 0.05) and indirectly (path coefficient = 0.45, p &lt; 0.001) by modulating the metabolic potential of carbon decomposition genes. These findings demonstrate that microbial‐driven ecological functionality reconfigures SOC molecular trajectories by coordinating the link between genetic potential and actual enzymatic performance, further evidenced by a fundamental ‘reversal’ in the relationship between SOC complexity and carbon stability. Vegetation succession redefines SOC molecular persistence by shifting the hierarchical control of microbial functional potential over SOC architecture. Our findings highlight that the link between microbial functionality and genetic potential dictates the non‐linear trajectory of SOC stabilization. The emphasizes microbial‐mediated MF as a central governor of soil carbon persistence, providing a new mechanistic framework for predicting long‐term carbon sequestration in subalpine forest ecosystems. Synthesis and applications . To optimize carbon sequestration, adaptive management should prioritize conserving broadleaf‐coniferous transition zones to bridge the ‘complexity minimum’ observed during succession. Utilizing microbial‐driven MF as a sensitive indicator enables early detection of carbon vulnerability, providing a science‐based tool for forest managers to sustain soil carbon persistence through targeted stand adjustments.