Global climate warming has led to the deepening of the active layer of permafrost on the Tibetan Plateau, further triggering thermal subsidence phenomena, which have profound effects on the carbon cycle of regional ecosystems. This study conducted warming (W) and thermal subsidence (RR) control experiments using an Open-Top Chamber (OTC) device in the river source wetlands of the Qinghai Lake basin. The aim was to assess the impacts of warming and thermal subsidence on soil temperature, volumetric water content, biomass, microbial diversity, and soil respiration (both autotrophic and heterotrophic respiration). The results indicate that warming significantly increased soil temperature, especially during the colder seasons, and thermal subsidence treatment further exacerbated this effect. Soil volumetric water content significantly decreased under thermal subsidence, with the RRW treatment having the most pronounced impact on moisture. Additionally, a microbial diversity analysis revealed that warming promoted bacterial richness in the surface soil, while thermal subsidence suppressed fungal community diversity. Soil respiration rates exhibited a unimodal curve during the growing season. Warming treatment significantly reduced autotrophic respiration rates, while thermal subsidence inhibited heterotrophic respiration. Further analysis indicated that under thermal subsidence treatment, soil respiration was most sensitive to temperature changes, with a Q10 value reaching 7.39, reflecting a strong response to climate warming. In summary, this study provides new scientific evidence for understanding the response mechanisms of soil carbon cycling in Tibetan Plateau wetlands to climate warming.