Nitrous oxide (N2O), a major greenhouse gas produced during denitrification, plays a significant role in global warming. Crop rotation can enhance soil nitrogen (N) use efficiency and influence N-transforming microbial communities, especially denitrifiers. This study investigated soils under four fertigated cropping systems in a semi-arid region of Northeast China: continuous soybean monocropping (SC), maize-soybean rotation (MS), maize-maize-soybean rotation (MMS), and maize-soybean-soybean rotation (MSS). The impact of these rotations on the abundance and community structure of nirS- and nirK-type denitrifiers was assessed using qPCR and highthroughput sequencing. Compared to the SC control, soybean rotation systems (MS, MMS, MSS) significantly increased soil nitrate reductase (NR) and nitrite reductase (NiR) activities while decreasing soil denitrification potential (SDP). Although the overall abundance of nirS- and nirK-type denitrifiers was generally lower in soybean rotations compared to the SC control, the nirS/nirK gene ratio was considerably higher, suggesting a potential reduction in N2O emissions. The community composition of both nirS- and nirK-type denitrifiers differed significantly between rotation and monocropping soils, with soil organic matter (SOM) serving as the primary driver. Soil nutrients influenced SDP indirectly by modulating denitrifier community structure, with nirStype denitrifiers contributing more prominently to denitrification. In conclusion, nirS-type denitrifiers played a more dominant role in denitrification, and maize-soybean rotations with fertigation significantly modified both the diversity and abundance of soil denitrifiers.