Drainage increases soil organic carbon (SOC) mineralization, but waterlogging will not necessarily slow the SOC decomposition. We investigated the effects of water regime (anaerobic vs. aerobic conditions) on SOC mineralization in adjacent wetland and grassland soils with contrasting biochemical properties in the east Tibetan Plateau. Biochemical characteristics of SOC (compositions of non-cellulosic and amino polysaccharides) were analyzed, then soils were moistened to 70% of water-holding capacity (aerobic) or saturated (anaerobic) and incubated at 25 °C for 95 days. The non-cellulosic sugar content in SOC was similar in wetland and meadow soils, but the mass ratio of hexoses (galactose plus mannose or rhamnose plus fucose) to pentoses (arabinose plus xylose) was three-fold greater in meadows than wetlands. Furthermore, there was three times more accumulation of microbial residues (sum of glucosamine, mannosamine, galactosamine, and muramic acid) in SOC, and more fungal than bacterial necromass in the meadow than wetland soils. This suggests slower transformation of plant litter by microorganisms, and thus less accumulation of microbial products in the SOC of wetlands than meadows. Meadow soils had more microbial biomass and higher activities of β–glucosidase, phenol oxidase, and urease per unit of SOC than wetland soils. During the 95-day incubation, C loss (as CO2) per unit of SOC was 55–73% greater in anaerobic than aerobic meadow soils, but was 59–64% less from wetland soils under anaerobic conditions than aerobic conditions. Thus, SOC decomposition in anaerobic conditions was dependent on the degree of SOC degradation, which was related to the initial proportion of plant and microbial residues. We addressed the importance of biochemical nature in regulating SOC decomposition under anaerobic conditions. We conclude that both the wetland drainage and grassland waterlogging increase SOC mineralization (measured as CO2 evolution) in alpine areas. © 2020 Elsevier Ltd