Perchlorate (ClO4) is recognized as an important contaminant in surface water and groundwater, which would pose health risks at very low concentrations. A methane-based membrane biofilm reactor (MBfR) has been successfully demonstrated for perchlorate reduction, which provided an alternative solution for perchlorate remediation with low cost. In this work, a multispecies biofilm model was developed to evaluate perchlorate reduction in the methane-based MBfR under different operational conditions. The model was calibrated and validated using the experimental data from the long-term operation of the MBfR at seven distinct stages. The results suggested that the developed model could satisfactorily describe perchlorate reduction and denitrification performances in the MBfR (R-2 > 0.9). The modeling results provided insight into the microbial community distribution in the biofilm, with aerobic methanotrophs and perchlorate reduction bacteria being mainly located at the membrane side (similar to 60%) and heterotrophic bacteria being situated near the liquid side (similar to 50%). The model simulations indicated that over 80% of perchlorate removal efficiency could be achieved through controlling the optimal combinations of methane pressure (P-CH4) and perchlorate loading (L-ClO4) (e.g., applying a P-CH4 of 30 kPa at a L-ClO4 of 0.08 g Cl/m(2)/d). In addition, the perchlorate reduction would be inhibited by the presence of nitrate and nitrite in the MBfR, which should be appropriately controlled during the future practical application of the promising process. (C) 2017 Elsevier B.V. All rights reserved.