Although subsurface contamination by organic chemicals is a pervasive environmental problem, a permeable reactive barrier (PRB) as a typical in-situ remediation technology is often successful at many sites. Laboratory tests have shown that perchloroethylene (PCE) can be dechlorinated by the combination of zero-valent iron and anaerobic microbial communities (FeMB), and the degradation pathway was: PCE -> TCE -> 1, 1-DCE -> ethylene -> ethane (Ma amd Wu Environ Geol 55(1):47-54, 2008). Based on Ma's experimental results, we have extended MT3DMS to simulate mother-daughter chain reactions using MODFLOW-2005 V1.7/MT3DMS V5.2. Second, using FeMB as multi-PRB's reactive media, a 5-component transport model for a three-dimensional aquifer contaminated by PCE subject to multi-PRB remediation was built. Third, the adsorption and degradation parameters of reactive media were estimated by means of genetic algorithm. Finally, the three-dimensional, homogeneous aquifer contaminated by PCE subject to multi-PRB remediation was simulated. Overall, the purpose of this paper was to use FeMB as multi-PRB's reactive media, and develop a modified MODFLOW/MT3DMS that can simulate a three-dimensional aquifer contaminated by PCE and its daughters. Results demonstrated that FeMB could be a potential reactive media for PCE-contaminated groundwater. Multi-PRB could be a preferred option for secondly pollution caused by application of one-stage PRB. The modified MODFLOW/MT3DMS can effectively simulate multispecies mother-daughter chain kinetic reactions. Sensitivity analysis showed that losses of reactivity and permeability may have a significant effect on remediation's success.