Aims <p>Soil microbial carbon use efficiency (CUE), defined as the fraction of assimilated organic carbon allocated to microbial biomass, plays a central role in soil carbon cycling. In paddy soils, irrigation regime and exogenous organic carbon (EOC) amendment jointly alter oxygen availability and substrate supply, which are expected to shift microbial carbon allocation between growth and respiration. However, how these management practices influence microbial CUE via microbial physiological processes remains poorly understood.</p> Methods <p>In this field experiment, straw and hydrochar were applied to paddy fields under flooding irrigation (FI) or controlled irrigation (CI) to assess their effects on dissolved organic carbon (DOC), microbial biomass carbon and nitrogen (MBC, MBN), microbial respiration (<i>R</i>_<i>s</i>), microbial growth and turnover, microbial community structure (PLFAs), and microbial CUE based on microbial growth measured by ¹⁸O-DNA incorporation.</p> Results <p>CI significantly increased soil MBC, MBN and DOC, accompanied by increases in <i>R</i>_<i>s</i> (33–47%) and microbial growth (229–320%), resulting in higher microbial CUE and turnover rates. EOC addition increased substrate availability, stimulating microbial growth (0.66–1.24-fold) more strongly than <i>R</i>_<i>s</i> (0.35–0.85-fold), thereby increasing CUE. Both CI and hydrochar addition significantly increased extracellular enzyme activities. Compared with straw, hydrochar more effectively promoted carbon allocation to microbial biomass while reducing respiration per unit of assimilated carbon. Random forest and path analyses revealed that CI and EOC inputs increased CUE mainly through enzyme-mediated stimulation of microbial growth rather than direct effects on respiration.</p> Conclusion <p>Overall, hydrochar combined with CI enhances microbial carbon retention, highlighting a promising management strategy for improving soil carbon accumulation in paddy soils.</p>