The transition from the vegetative stage to reproductive stage of plants and variations in soil water regimes can alter the community feedbacks of rhizosphere microbiomes by affecting the partitioning of photosynthates to roots. However, little is known about how different rhizosphere microbiota respond to the growth stages of drought-resistant crops under different irrigation regimes. To address these issues, we investigated the effects of irrigation regimes on the rhizosphere prokaryotic and fungal communities at the pre- and post-anthesis stages of oats in a semi-arid region of northeastern China. The prokaryotic and fungal community traits of the oat rhizosphere were characterized by Illumina high-throughput sequencing. The results revealed that the prokaryotic diversity was primarily regulated by oat growth stage, while the fungal diversity was mainly increased by irrigation regimes. Similarly, all prokaryotic phyla responded significantly to oat growth stages rather than irrigation regimes, while the composition of the fungal taxa was largely regulated by irrigation regimes. Approximately 2–3-fold higher proportions of the predominating pathogenic Fusarium genus were identified under dryland farming conditions than under irrigation treatment. In addition, functional predictions suggested that the contrasting responsive traits of prokaryotes and fungi were attributed to their functional guilds, which were related to oat growth stages and soil water conditions. However, the properties of the prokaryotic networks mainly responded to irrigation regimes while the fungal networks were regulated by oat growth, implying distinct determination mechanisms for microbial diversity and community stability. Our results indicate that rhizosphere prokaryotic and fungal communities differentially responded to oat growth stages and soil water history, highlighting the significance of irrigation in manipulating rhizosphere microbes in semi-arid regions.