Climate models predict that droughts will increase in Southeast Asia, yet little is known about how soil respiration (Rs) and its components heterotrophic respiration (Rh) and autotrophic respiration (Ra) will change following drought years. To clarify this issue and to detect underlying mechanisms, we conducted a 2-year field experiment in the seventh and eighth year of long-term artificially droughted plots within a tropical rainforest in Xishuangbanna, southwest China. We separated Rh and Ra by trenching and we measured dissolved organic carbon in the soil and microbial biomass. In average, the drought stress, reduced through-fall by 50%, reduced fine root biomass by 36%. Although Ra declined by 35%, active inorganic N and Rh increased by 31% and 29%. Further, the coefficient of determination (R-2) between soil microbial community composition, mainly, group-specific phospholipid fatty acid and the variation of Rh was among 17%-59% during the dry and rainy season of 2018. However, changes in dissolved organic carbon, microbial biomass carbon and nitrogen, ammonium nitrogen, were inconsistent with the increase in Rh. There was an inconsistent significant positive correlation between seasonal change of CO2 flux and these processes dynamic across 2017 and 2018. Soil temperature, soil moisture, and litterfall jointly determined annual variation in Rs and Rh across two years. These findings have improved understanding of how long-term drought stress influences soil CO2 effluxes via change of soil-based biochemical indicators (like fine root, active inorganic nitrogen, and soil microorganisms).