Introduction Nitrification inhibitors and straw incorporation are used to reduce microbial mediated nitrogen (N) losses, thereby increasing N use efficiency (NUE) in cropland soil, but their effects on nitrous oxide (N2O) emission across different soil types and the underlying molecular mechanisms remain less understood. Materials and Methods In this study, we investigated how nitrification inhibitor nitrapyrin and straw incorporation affected soil N balance, N2O emission, nitrifiers and denitrifiers in three cropland soils (black, fluvo‐aquic and red soils). Results Compared with fertilization‐only treatment (N), nitrapyrin addition increased ammonium, while it decreased nitrate concentration in all soils; however, the performance of straw incorporation was less significant. Nitrapyrin decreased N2O emission only in the fluvo‐aquic soil, while straw incorporation strongly increased N2O emission in the red soil. Terminal restriction fragment length polymorphism analysis revealed that the denitrifier community was distinct across the three soils, but not strongly structured by nitrapyrin or straw incorporation. Compared with the N treatment, straw incorporation and nitrapyrin increased nosZ gene abundance only in the black soil. Structural equational modelling further confirmed that, after accounting for different soil properties, straw incorporation significantly increased N2O emission from black and red soils, and a decrease in nosZ gene abundance was the main biological factor for increased N2O emission in red soil. Conclusion Taken together, our work provides new knowledge that the performance of nitrification inhibitor and straw incorporation on N2O emission is soil type‐dependent, and management practices should be used as per soil type to balance NUE and N2O emission.