Nitrogen reduction, in association with increased planting density and irrigation management, has been widely adopted in super rice cultivation systems to pursue higher yield with lower input. Here, soil microbial community structures under accurate N and water management were investigated after four years of experiments. Plot experiments were conducted with three treatments, including conventional farming practice (CF), reduced nitrogen with increased plant density (RNID), and reduced nitrogen with increased plant density and precise irrigation (RNIDPI). The results showed that RNID treatment increased soil bacterial diversity, enriched biomarker bacterial taxa, and altered bacterial community structure, with pH as the influential factor. The phylum Chloroflexi was enriched in the treatment of N reduction, while a higher ratio of Firmicutes was present in CF treatments. RNID treatment witnessed a low proportion of bacterial functional groups involved in nitrification and nitrate reduction. N fertilizer reduction with irrigation management increased rice yield (up to 22%) without changing the major soil fertility properties except for the increased pH and decreased ammonium N. The results suggest that N reduction, in association with increased plant density and accurate irrigation, is beneficial for super rice production.