The Tibetan grasslands store 2.5% of the Earth's soil organic carbon. Unsound management practices and climate change have resulted in widespread grassland degradation, providing open habitats for rodent activities. Rodent bioturbation loosens topsoil, reduces productivity, changes soil nutrient conditions, and consequently influences the soil organic carbon stocks of the Tibetan grasslands. However, these effects have not been quantified. Here, using meta-analysis and upscaling approaches, we found that rodent bioturbation impacts on the Tibetan grassland soil organic carbon contents were depth-dependent, with significant (p < 0.001) decreasing of 24.4% in the topsoil (0–10 cm) but significant (p < 0.05) increasing of 35.9% in the deeper soil layer (40–50 cm), and nonsignificant changes in other soil layers. The depth-dependent responses in soil organic carbon content were closely associated with rodent tunnel burrowing, foraging, excrement deposition, and mixing of the upper and deeper soil layers. Rodent bioturbation shown nonsignificant impacts on soil bulk density, independent of soil layer. Tibetan grasslands totally lose –35.2 Tg C yr–1 (95% CI: –48.5 to –21.1 Tg C yr–1) and –32.9 Tg C yr–1 (–54.2 to –8.6 Tg C yr–1) due to rodent bioturbation in the 0–10 cm or 0–30 cm soil layer while no significant net loss was found over the 0–90 cm layer. Our findings highlight the importance of considering depth-dependent factors to robustly quantify the net changes in the terrestrial soil organic carbon stocks resulting from disturbances such as rodent bioturbation.