Applying the permeable reactive barrier (PRB) to remedy the contaminated groundwater is a fast emerging technology for in situ remediation of contaminated groundwater, and it has many advantages over the traditional methods of ex situ treatment. The mathematical simulation of the remediation by PRB is a useful tool for optimizing the barrier design, predicting the remove process and evaluating the efficiency of remediation. In this paper, the mathematical models of special PRB system were presented, which can be used to simulate the removal process of methyl tertiary butyl ether (MTBE) from groundwater by using a biological permeable reactive barrier. The average error of 5.74% between the simulated results and the experimental data obtained from experimental test column shows that the models proposed are available. Moreover, as seen from the distribution of MTBE concentration in the computation domain, parts of contaminated groundwater flow into the barrier through its two side surfaces and form shortcut flow paths through the barrier, and the MTBE in those shortcut flows can not be fully degraded. As a result, after treating, the MTBE concentration of the treated groundwater flowing near the two side region of the biological permeable reactive barrier is higher than that of the flow flowing through the center region of the PRB. Knowing above phenomena will be helpful for PRB system design to remedy the MTBE contamination of the groundwater.