Periphytic biofilm reactor (PBfR) shows great potential in pollutants removal. However, few studies were focused on mathematical model of pollutants removal in PBfR. A three-step PBfR was designed and a new model was developed to simulate the kinetics of Cu and Cd removal from simulated wastewater. The results show that the PBfR could remove 99.0% Cu and 99.7% Cd from liquid wastewater. The experiment data could be well fitted with a high correlation coefficients both for Cu and Cd. The microbial community in the PBfR could be selfadjusted to tolerate the toxicities of Cu and Cd, resulting in sustainable and high decontamination efficiencies. The eukaryote in the PBfR played a vital role in Cu and Cd removal. The prokaryote showed negative effect on Cu and Cd removal, though it had more diversity than eukaryote. This study provides a new approach for Cu and Cd removal and their kinetics simulation in photoautotrophic bioreactor.