A 28-day microcosm experiment was conducted using three paddy soils (an alluvial paddy soil, a loess-formed paddy soil, and a yellow clayey paddy soil) to investigate the impact of procyanidin on N2O emissions and associated microbial mechanisms. The efficacy of procyanidin on N2O emissions varied among the paddy soils tested, with an average inhibition rate ranging from 2.7% in the alluvial paddy soil to 57.1% in the loess-formed paddy soil. Furthermore, suppression of N2O emissions by procyanidin occurred alongside fluctuations in nitrate reductase activity and nirS- and nirK-type denitrifiers abundance. The correlation analysis indicates that nitrate reductase, clade I nirS-denitrifiers, clade I or II, and clade III nirK-denitrifiers were closely linked to N2O emissions. These findings provide evidence that procyanidin is capable of limiting N2O emissions in paddy soils by inhibiting nitrate reductase and different clades of nirS-/nirK-denitrifiers.