AbstractMicrobial residues contribute to the long‐term stabilization of carbon in the entire soil profile, helping to regulate the climate of the planet; however, how sensitive these residues are to climatic seasonality remains virtually unknown, especially for deep soils across environmental gradients. Here, we investigated the changes of microbial residues along soil profiles (0–100 cm) from 44 typical ecosystems with a wide range of climates (~3100 km transects across China). Our results showed that microbial residues account for a larger portion of soil carbon in deeper (60–100 cm) vs. shallower (0–30 and 30–60 cm) soils. Moreover, we find that climate especially challenges the accumulation of microbial residues in deep soils, while soil properties and climate share their roles in controlling the residue accumulation in surface soils. Climatic seasonality, including positive correlations with summer precipitation and maximum monthly precipitation, as well as negative correlations with temperature annual range, are important factors explaining microbial residue accumulation in deep soils across China. In particular, summer precipitation is the key regulator of microbial‐driven carbon stability in deep soils, which has 37.2% of relative independent effects on deep‐soil microbial residue accumulation. Our work provides novel insights into the importance of climatic seasonality in driving the stabilization of microbial residues in deep soils, challenging the idea that deep soils as long‐term carbon reservoirs can buffer climate change.