Transforming gypsum into α-calcium sulfate hemihydrate (α-HH) provides a promising utilization pathway for the abundant amount of chemical gypsum. The transformation follows the route of “dissolution-recrystallization”, during which the arsenic pollutant in gypsum is released into the solution, and hence raises the possibility of being distributed into the product of α-HH, a potential harm that has always been neglected. Investigation of the transformation process at neutral pH revealed that the arsenate ions in solution were distributed into α-HH and generated an enrichment of arsenic by 4–6 times. Arsenate ions distributed into α-HH by substitution for lattice sulfate, adsorption on α-HH facets and occupation for surface sulfate sites. While at higher concentrations, calcium arsenate coprecipitated with α-HH or even crystallized independently. Increasing temperature accelerated the phase transformation and restrained arsenate migration into α-HH due to the lag of distribution balance. The pH of solution modulated the dominant arsenate species and decreasing pH weakened arsenate substitution capacity for sulfate in α-HH. This work uncovers arsenate distribution mechanism during the transformation of gypsum into α-HH and provides a feasible method to restrain arsenate distribution into product, which helps to understand arsenate behavior in hydrothermal solution with high concentration of sulfate minerals and provides a guidance for controlling pollutants distribution into product.