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Soil microbes are both drivers and contributors of soil organic C (SOC) dynamics. However, information on how the multiple co-occurring environmental changes affecting microbial community and residues is unclear. Here, we measured phospholipid fatty acids and amino sugars (ASs) to explore how soil microbial community and residues changed under soil warming, throughfall reduction, root exclusion and their interactions in a natural deciduous broad-leaved oak forest. Soil warming significantly increased the Gram-positive to Gram-negative bacteria (G + /G - ) ratio, and its interaction with root exclusion significantly reduced fungi-to-bacteria (F/B) ratio but stimulated the contributions of ASs to SOC (AS/SOC). Throughfall reduction also marginally increased G + /G - and AS/SOC, and suppressed F/B ratio. However, no interactive effects of soil warming and throughfall reduction on soil microbial community and residues were observed. Light fraction organic C and inorganic nitrogen were the key drivers in regulating the variation in the microbial community structure, and SOC was the controlling factor of microbial residue accumulations. Hence, soil C quality instead of water dominates the responses of microbial community structure and residues contribution to SOC to soil warming. Our results highlight the importance of soil substrate quality when predicting the terrestrial climate-C feedback.