Periphyton, composed of diatoms, green algae, bacteria, protozoa, metazoans, epiphytes, and detritus, is widely distributed in paddy soil. It has been studied that the periphyton could significantly affect the behavior of heavy metals in water environment. However, the interactions between the periphyton and arsenic in paddy soil have been reported rarely. In this study, model paddy ecosystems with periphyton or not were built to explore the effects of periphyton on the bioavailability and transformation of arsenic in paddy soil. Further, the accumulation of arsenic in each part of rice were analyzed. Results showed that the periphyton on the surface of paddy soil could significantly increase the pH and decrease the Eh in tillering and heading stage in soil, but significantly decrease the pH and increase Eh in maturing stage in soil. The arsenic content in the periphyton fluctuated from 137.9 to 272.4 mg kg^-1, resulting in a significant and substantial decrease in arsenic concentration in pore water of topsoil. Fourier transform-infrared (FT-IR) analysis confirm that the polysaccharides, hydroxyl (-OH), and amide (N-H) were responsible for arsenic binding in periphyton. In the maturing stage, the periphyton could reduce the formation of iron plaque in rice root and the content of arsenic in the iron plaque, but has no significant effect on the accumulation of arsenic in root and shoot of rice from tillering stage to maturing stage. The results in the present study suggest that the periphyton mainly affects the bioavailability and transformation of arsenic in topsoil.