Soil microbes are essential links between above- and below-ground ecosystems and play an important role in regulating ecological functions in the soil. Dynamic interactions within the soil-microbial community in a cereal-legume intercropping ecosystem influence the composition and structure of N-cycling microbial groups (e.g. nitrogen-fixing bacteria). However, these effects have not been extensively studied in some intercropping patterns or in response to varying nitrogen fertilization levels. In the present study, we evaluated the effects of reduced and conventional nitrogen application in a sweet maize (Zea may L.)/soybean (Glycine max L.) strip intercropping system under three cropping patterns over a 3-year time period. High-throughput sequencing and quantitative PCR techniques were used to investigate changes to both the microbial community structure and the expression of key nitrogen-cycling genes in the rhizosphere. Our results indicate that reduced nitrogen application affected the microbial community structure in the rhizosphere, but microbial diversity in the sweet maize rhizosphere was relatively stable. Both the abundance and activity of functional marker genes for microbial nitrogen fixation (nifH), nitrification (amoA), denitrification (nirS, nirK, nosZ), and decomposition (chiA) increased significantly from 2013 to 2016. Taken together, these data demonstrate that the quantified shifts in the soil microbial community and the observed increases in the expression of key functional genes involved in N-cycling were the result of reduced nitrogen application in this strip intercropping system. This study, therefore, provides essential insight into the potential relationships between functional nitrogen-cycling genes and mitigation of nitrogen-loss and N2O emissions in a cereal-legume strip intercropping system.