Background:There are many studies on disentangling the responses of autotrophic (AR) and heterotrophic (HR) respiration components of soil respiration (SR) to long-term drought, but few studies have focused on the mechanisms underlying its responses. Methods:To explore the impact of prolonged drought on AR and HR, we conducted the 2-year measurements on soil CO2 effluxes in the 7th and 8th year of manipulated throughfall reduction (TFR) in a warm-temperate oak forest. Results:Our results showed long-term TFR decreased HR, which was positively related to bacterial richness. More importantly, some bacterial taxa such as Novosphingobium and norank Acidimicrobiia, and fungal Leptobacillium were identified as major drivers of HR. In contrast, long-term TFR increased AR due to the increased fine root biomass and production. The increased AR accompanied by decreased HR appeared to counteract each other, and subsequently resulted in the unchanged SR under the TFR. Conclusions:Our study shows that HR and AR respond in the opposite directions to long-term TFR. Soil microorganisms and fine roots account for the respective mechanisms underlying the divergent responses of HR and AR to long-term TFR. This highlights the contrasting responses of AR and HR to prolonged drought should be taken into account when predicting soil CO2 effluxes under future droughts.