The growth and development of pitaya are closely associated with the rhizosphere microbiome, yet there is a lack of understanding regarding the seasonal characteristics of the microorganisms during the fruit’s production cycle. This study focused on the red-fleshed pitaya in Hainan, utilizing high-throughput sequencing technology to investigate the dynamics of the rhizosphere microbial community across different seasons and its correlation with soil physicochemical factors. The results indicated that the richness and diversity of the pitaya rhizosphere microbial community were seasonally driven. There were significant differences in the Ace index, Chao1 index, Shannon index, and Simpson index among the microbial communities across seasons, particularly showing an increasing trend in autumn. A total of 6132 bacterial OTUs and 1850 fungal OTUs were obtained from 12 rhizosphere samples collected throughout the four seasons. Bacterial OTUs were classified into 43 phyla, 135 classes, 319 orders, 502 families, and 963 genera, while fungal OTUs were classified into 15 phyla, 42 classes, 103 orders, 214 families, and 423 genera. The phyla Firmicutes, Actinobacteria, and Proteobacteria showed stable and dominant relative abundances across the four seasons, making them the predominant bacterial phyla. The genus Bacillus maintained the highest relative abundance within the bacterial community, making it the dominant bacterial genus; however, its relative abundance was significantly higher in spring and winter compared to summer and autumn. The phylum Ascomycota was the dominant fungal phylum in the pitaya rhizosphere. The genus Chaetomium was the dominant fungal genus, with a notably higher relative abundance in spring compared to other seasons. Differential species analysis revealed 15 bacterial differential species and 3 fungal differential species across the four seasons. The physicochemical properties of the pitaya rhizosphere soil showed significant seasonal variation and were closely related to the rhizosphere microbial community. FAPROTAX predictions indicated that the pitaya rhizosphere bacteria primarily exhibited functions such as chemoheterotrophy, aerobic chemoheterotrophy, ureolysis, nitrate reduction, cellulolysis, nitrogen fixation, aromatic compound degradation and animal parasites or symbionts. FUNguild predictions showed that the pitaya rhizosphere fungi mainly displayed saprotrophic lifestyles and some unknown functions. In summary, this study demonstrated that the structure of the rhizosphere microbial community associated with red-fleshed pitaya in Hainan undergoes significant changes across the four seasons, with the highest diversity and richness observed in the fall. Bacillus and Chaetomium were identified as the dominant bacterial and fungal genera in the rhizosphere, respectively. The findings could provide a theoretical basis for designing cultivation improvement measures based on rhizosphere microbiota for pitaya.