Schwertmannite (Sch) holds a great promise as an iron material for remediating Arsenic (As)-contaminated paddy soils, due to its extremely high immobilization capacities for both arsenate [As(V)] and arsenite [As(III)]. However, there is still limited knowledge on the mineral phase transformation of this metastable iron-oxyhydroxysulfate mineral in paddy soils, particularly under different water management regimes including aerobic, intermittent flooding, and continuous flooding, and how its phase transformation impacts the migration of As in paddy soils. In this study, a membrane coated with schwertmannite was first developed to directly reflect the phase transformation of bulk schwertmannite applied to paddy soils. A soil incubation experiment was then conducted to investigate the mineral phase transformation of schwertmannite in paddy soils under different water management regimes and its impact on the migration of As in paddy soil. Our findings revealed that schwertmannite can persist in the paddy soil for 90 days in the aerobic group, whereas in the continuous flooding and intermittent flooding groups, schwertmannite transformed into goethite, with the degree or rate of mineral phase transformation being 5% Sch >1% Sch > control. These results indicated that water management practices and the amount of schwertmannite applied were the primary factors determining the occurrence and degree of mineral transformation of schwertmannite in paddy soil. Moreover, despite undergoing phase transformation, schwertmannite still significantly reduced the porewater As (As(III) and As(V)), and facilitated the transfer of non-specifically adsorbed As (F1) and specifically adsorbed As (F2) to amorphous iron oxide-bound As (F3), effectively reducing the bioavailability of soil As. These findings contribute to a better understanding of the mineralogical transformation of schwertmannite in paddy soils and the impact of mineral phase transformation on the retention of As in soil, which carry important implications for the application of schwertmannite in remediating As-contaminated paddy soils.