The soils of alpine meadows on the Tibetan Plateau act as significant carbon reservoirs and are particularly vulnerable to warming. Nevertheless, the long-term (≥20 years) warming impact on SOC composition and deep soil dynamics in alpine meadows remains unclear. This study explored the effects of two decades of warming using open-top chambers on various aspects of alpine meadow ecosystems, including plant community composition and biomass, soil physicochemical characteristics, microbial communities, and SOC content in both bulk soil and its fractions. Prolonged warming had no impact on plant-derived C inputs, as indicated by both unchanged above- and below-ground biomass, but it reduced the light fraction carbon (LF-C) in the surface soil layer (0−10 cm) by 25%, with no notable changes observed in bulk SOC or heavy fraction carbon (HF-C) in the surface soil as well as deeper soil layers (10−50 cm). Additionally, long-term warming caused a notable rise in fungal-derived residues and an increase in aromatic carbon, while concurrently decreasing alkyl carbon in the surface soils. These findings imply that prolonged warming acce-lerates the breakdown of more readily decomposable organic matter, shifting the SOC pool towards a more chemically resistant state, even though there was no net change in bulk SOC.