To reveal the differences in the effects and mechanisms of different biological nitrification inhibitors (BNIs) on N₂O emissions from red paddy soil, a 21-day soil column flooding incubation experiment was conducted to compare three BNIs, 1,9-decanediol (1,9-D), linolenic acid (LN) and methyl 3-(4-hydroxyphenyl)propionate (MHPP) with the chemically synthesized nitrification inhibitor dicyandiamide (DCD) on soil N₂O emissions and associated nitrification and denitrification functional genes. The results showed that the different BNIs (1,9-D, LN, MHPP) significantly reduced peak N₂O emissions by 40.1% on average; 1,9-D and MHPP suppressed total N2O emissions by 44.5% and 43.9%, respectively, while DCD and LN had no significant effects. Both 1,9-D and MHPP differed in their regulations of nitrifying and denitrifying bacteria, with 1,9-D inhibiting the growth of both AOA, AOB, and nirS microorganisms; MHPP only inhibited the growth of AOA; whereas the abundance of AOA-amoA and nirS genes were significant and positively correlated with soil N₂O emissions. Meanwhile, both 1,9-D and MHPP increased nosZ gene abundances and their ratios to AOA-amoA+AOB-amoA, nirS+nirK and AOA-amoA+AOB-amoA+nirS+nirK, which were significantly negatively correlated with soil N₂O emissions. In conclusion, changes in the abundance of AOA-amoA and nosZ genes caused by the biological nitrification inhibitors 1,9-D and MHPP play important roles in N₂O reduction in red paddy soil.