Soil respiration affects the global carbon cycle, and wetland water level is closely related to soil respiration. However, due to the limited in situ observations, it is unclear how alpine marsh soil respiration and its components respond to falling water levels. Establishing an experimental platform for water level decline control in the Naleqiao march of the Ruoergai Plateau, we conducted in situ monitoring of the changes of soil respiration and its components, and preliminarily explored the potential relationship between soil respiration and its components and biotic and abiotic factors. The results showed that the decrease in water level did not have a significant effect on soil respiration (Rs) in alpine marsh, but autotrophic respiration (Ra) and heterotrophic respiration (Rh) showed significantly different responses to water table drawdown. Among them, the autotrophic respiration rate decreased by 67.2%, and the heterotrophic respiration rate increased by 67.3%. The proportion of heterotrophic respiration and autotrophic respiration in soil respiration changed significantly. After the water table drawdown, Rh/Rs increased by 88% compared with the control, and Ra/Rs decreased by 61%. The driving factors of autotrophic respiration and heterotrophic respiration caused by water level decline were different. The plant height, aboveground and underground biomass explained the changes of autotrophic respiration, and soil temperature and C:N were the key influencing factors of the heterotrophic respiration. The study shows that there are significant differences in the intensity of the effects of water level decline on soil respiration components and their drivers in alpine marsh ecosystems, which need to be considered in terrestrial surface carbon cycle models to better assess the feedback effect of alpine herbaceous marsh carbon cycle on climate change.