Photosynthesis and microbial sulfate reduction are the two key biogeochemical processes which control the global carbon cycle in Earth history. While geochemical signatures of these metabolisms are ambiguous in carbonate rocks, the emergence of carbonate dual clumped isotope (Δ₄₇ and Δ₄₈) can shed on whether biogeochemical processes are sensitive to the kinetic isotope effects induced by microbial metabolism and hence identify these in the geological record. Here we applied dual clumped isotopes to decipher, photosynthesis and microbial sulfate reduction during the formation of the lacustrine carbonates in the western part of Qaidam Basin. This bioherm skeleton is comprised of low-Mg calcites and coated by isopachous dolomite cement. After a chemical separation leached by buffered-acetic acid, the skeletal low-Mg calcites have the positive disequilibrium of Δ₄₈ values than the expected, but the Δ₄₈ values of dolomite cements show the negative disequilibrium. The positive Δ₄₈-disequilibrium of the skeletal low-Mg calcites is probably attributed to the photosynthesis which can remove CO₂ from the surrounding water and, resultantly, enhance pH and saturation state. In contrast, the isopachous dolomite cement may be a product microbial sulfate reduction which was suggested to induce the disequilibrium as a result of CO₂ hydration/hydroxylation (Lu et al., 2025; Lu and Swart, 2024). This study highlights the importance of kinetic isotope effects in deciphering geochemical signals of modern and ancient carbonate rocks.