Global warming increases the freeze-thaw (FT) cycles, however, the impact of increased FT cycles on the environmental behavior of arsenic (As) in soils and the toxic effect of As to microorganisms are still unknown. Herein, the influence of FT cycles on As forms, available As, and microbial community structure in paddy soils was investigated. After 60 FT cycles, the content of exchangeable As and residual state As decreased by 1.77% and 14.18%, respectively, while the carbonate-bound As, iron-manganese oxide-bound As, and organic-bound As increased by 4.53%, 6.5%, and 5.35%, respectively. The available As in soil and As(III) in soil water increased by 6.53 mg/kg and 38.9 μg/L, respectively. High throughput sequencing data indicated that FT cycles reduced Alpha diversity and significantly changed Beta diversity of soil microorganisms. FT cycles considerably enhanced the relative abundance of Sphingomonas and Lysobacter. Kyoto Encyclopedia of Genes and Genomes function predictions revealed that FT cycles significantly activated cellular gene segments involved in soil bacterial immunological disorders, cell motility, parasite infectious diseases, and neurological diseases. This study would serve as a reference for future study on environmental behavior and toxic effects of heavy metals in farm soils of seasonal FT aeras.