【Objective】Application of biological nitrification inhibitors (BNIs) is an effective strategy to suppress nitrification rates and mitigate nitrous oxide (N?O) emissions in agricultural soils. However, how the addition of BNIs affects soil nitrification rate and N?O emission under organic fertilizer application remains unclear. 【Method】The microcosm aerobic incubation experiment was conducted using upland red and black soils, with two levels of organic fertilizer (chicken manure: N 0 and 100 mg·kg?1 soil) and three levels of BNIs addition (1,9-decanediol: 0, 1,000, and 2,000 mg·kg?1 soil). During the incubation, concentrations of inorganic nitrogen (N) and N?O emissions were measured, and quantitative PCR was employed to analyze microbial gene abundances related to N transformation. 【Result】The addition of 1,9-decanediol significantly decreased the net nitrification rate in both soils regardless of organic fertilizer input (P<0.05), exhibiting a dose-dependent suppression effect. Specifically, with organic fertilizer input, high concentrations of 1,9-decanediol decreased the net nitrification rate in black soil by 79% and even shifted the net nitrification rate in red soil from positive to negative. In contrast to nitrification, the addition of 1,9-decanediol either low or high concentrations significantly elevated N?O emissions in both soils, irrespective of organic fertilizer input (P<0.05). Also, a dose-dependent stimulation of N?O emissions occurred only in black soil. In red soil with and without organic fertilizer input, 1,9-decanediol significantly reduced the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) amoA genes (P<0.05), with greater suppression at higher doses. In contrast, the suppressive effect in black soil was significantly weaker than in red soil. Regardless of organic fertilizer application, only high dosage of 1,9-decanediol significantly reduced the abundance of key denitrifying genes in red soil. In addition, partial least squares regression analysis indicated that under organic fertilizer plus BNIs treatment, net N mineralization rate and AOA/AOB amoA abundances were identified as primary determinants of nitrification rates, while net nitrification and mineralization rates were key drivers of N?O emissions. Net nitrification rate was significantly negatively correlated with N?O emissions (P<0.05), suggesting that denitrification rather than nitrification is the major pathway of N?O production. 【Conclusion】Combined application of organic fertilizer with biological nitrification inhibitor significantly reduced nitrification rates in red and black soils, but significantly enhanced N?O emissions. Therefore, rational selection of BNIs types and application rates is critical to avoid paradoxically stimulating N?O emissions while suppressing nitrification in upland agricultural soils.