The unclear turnover of soluble and solid phases of biochar during increasingly severe climate change (e.g., intensive rainfall) raised questions about the carbon stability of biochar in soil. Here, we present an in-depth analysis of the molecular-level transformations occurring in both the soluble and solid phases of biochar subjected to prolonged wet-dry cycles with simulated rainwater. Biochar properties, including surface functionality and carbon texture, greatly affected the transformation route and led to a distinct stability variation. The rich alkyl −CH3 on the low-temperature biochar (450 °C) was oxidized to hydroxymethyl −CH2OH or formyl −CHO, and the ester −COOC− or peptide −CONHC− bonds were fragmented in the meantime, causing the release of protein- or lipid-like organic carbon and the declined carbon stability (Æ, tested by H2O2 oxidation, from 60.1% to 53.2%). After a high-temperature (750 °C) pyrolysis process, only oxidation of the surface −OH with limited bond breaking occurred after rainwater elution, presenting a marginal composition difference with constant stability. However, the fragile carbon nature of biochar, caused by CO2 activation, led to enhanced fragmentation, oxidation, and hydration, resulting in the release of tannin-like organic carbon, which compromised the carbon storage (Æ decreased from 81.2% to 73.0%). Our findings evaluated the critical transformation of biochar during intensive rainfall, offering crucial insights for designing sustainable biochar and achieving carbon neutrality.