Tunnels construction are widely used to facilitate large transport infrastructure projects, which may lead to a significant impact on soil organic carbon (SOC) dynamics and SOC chemical stability through depleting groundwater. However, the mechanisms of the effects tunnel construction on the chemical stability of SOC remain unexplored, which has become one of the most important but the least studied field. Therefore, this study aimed to investigate how tunnel construction impacts the chemical stability of SOC in shrublands along three altitude gradients (3240, 3420 and 3600 m above sea level) in the Eastern Tibetan Plateau. The results showed that tunnel construction did not significantly change SOC and its fractions regardless of altitude levels. However, tunnel construction increased O-alkyl carbon (C) by 10-15%, and decreased alkyl C (8-13%) and aromatic C (8-12%). These changes reduced SOC disintegration (alkyl C/O-alkyl C) and increased aliphaticity (aliphatic C/aromatic C) along three altitudes, causing a decrease in the chemical stability of SOC. This phenomenon was attributed to the reduced microbial activity caused by the decrease in soil water content after tunnel construction and an increase in active functional groups due to the increase of fine root biomass revealed by structural equation model. Our finding suggests that tunnel construction had no impact on SOC content, but the reduction in chemical stability of SOC may have a profound impact on long-term SOC sequestration. These findings offered new insights in predicting long-term SOC dynamics following giant construction engineering.