Understanding the balance between alkalinity generation from carbonate and silicate weathering, and the effect of sulfide weathering, is crucial for comprehending the impact of these processes on atmospheric CO2 levels. However, the sequestration potential and the net balance of CO2 between the release from sulfide weathering and the consumption by silicate weathering in permafrost environments remain contentious. This study examines the Shaliu River, a typical permafrost-dominated headwater catchment in the Northeast Tibetan Plateau, from a micro-watershed perspective to elucidate the effects of permafrost on chemical weathering and CO2 budgets during ablation period. Silicate weathering in the Shaliu River contributes 25–32 % to solute load, while carbonate weathering contributes 39–45 %. Sulfuric acid (H2SO4) plays a key role in carbonate weathering, accounting for 74 % of it and 37 % of the river’s solute load, especially in the permafrost-covered upstream areas. In contrast, bicarbonate (HCO3–) impacts are more evident in the lower reaches without permafrost. By integrating silicate and carbonate weathering with H2SO4-driven reactions, CO2 budget analysis indicates that the Shaliu River basin acts as a carbon source. The MEANDIR inversion model consistently depicts the watershed as a carbon source, influenced by permafrost and lithology. This implies that sulfide oxidation to produce sulfuric acid (H2SO4) drives carbonate weathering may significantly counterbalance the carbon sequestration associated with silicate weathering over geological timescales. The study provides a comprehensive understanding of the carbon budget dynamics within the permafrost-dominated watersheds of the Tibetan Plateau, enhancing the comprehension of carbon cycle processes in high-altitude ecosystems.