Prolonged drought results in serious ecological consequences in forest ecosystems, particularly for soil microbial communities. However, much is unknown about soil microbial communities in their response to long-term consecutive droughts in warm-temperate forests. Here, we conducted a 7-year manipulated throughfall reduction experiment (TFR) to examine the responses of bacterial and fungal communities in terms of richness and networks. Our results show that long-term TFR reduced bacterial, but not fungal, richness, with rare bacterial taxa being more sensitive to TFR than dominant taxa. The bacterial network under the TFR treatment featured a simpler network structure and fewer competitive links compared to the control, implying weakened interactions among bacterial species. Bacterial genes involved in xenobiotic biodegradation and metabolism, and lignin-degrading enzymes were enhanced under TFR treatment, which may be attributed to TFR-induced increases in fine root biomass and turnover. Our results indicate that soil bacterial communities are more responsive than fungi to long-term TFR in a warm-temperate oak forest, leading to potential consequences such as the degradation of recalcitrant organics in soil.