Dynamic nitrification and denitrification processes are affected by changes in soil redox conditions, and they play a vital role in regulating soil N₂O emissions in rice-based cultivation.  It is imperative to understand the influences of different upland crop planting systems on soil N₂O emissions.  In this study, we focused on two representative rotation systems in Central China: rapeseed–rice (RR) and wheat–rice (WR).  We examined the biotic and abiotic processes underlying the impacts of these upland plantings on soil N₂O emissions.  The results revealed that during the rapeseed-cultivated seasons in the RR rotation system, the average N₂O emissions were 1.24±0.20 and 0.81±0.11 kg N ha^–1 for the first and second seasons, respectively.  These values were comparable to the N₂O emissions observed during the first and second wheat-cultivated seasons in the WR rotation system (0.98±0.25 and 0.70±0.04 kg N ha^–1, respectively).  This suggests that upland cultivation has minimal impacts on soil N₂O emissions in the two rotation systems.  Strong positive correlations were found between N₂O fluxes and soil ammonium (NH₄⁺), nitrate (NO₃^–), microbial biomass nitrogen (MBN), and the ratio of soil dissolved organic carbon (DOC) to NO₃^– in both RR and WR rotation systems.  Moreover, the presence of the AOA-amoA and nirK genes were positively associated with soil N₂O fluxes in the RR and WR systems, respectively.  This implies that these genes may have different potential roles in facilitating microbial N₂O production in various upland plantation models.  By using a structural equation model, we found that soil moisture, mineral N, MBN, and the AOA-amoA gene accounted for over 50% of the effects on N₂O emissions in the RR rotation system.  In the WR rotation system, soil moisture, mineral N, MBN, and the AOA-amoA and nirK genes had a combined impact of over 70% on N₂O emissions.  These findings demonstrate the interactive effects of functional genes and soil factors, including soil physical characteristics, available carbon and nitrogen, and their ratio, on soil N₂O emissions during upland cultivation seasons under rice-upland rotations.