With the continuous development of groundwater remediation technologies for contaminated sites, selecting appropriate remediation technologies and evaluating their effectiveness are the keys to achieving water resource protection and sustainable utilization. In this paper, the groundwater remediation process was simulated by the finite difference method, and the effect of remediation by permeable reaction wall (PRB) coupled with pumping-injection hydraulic control technology was evaluated. The study used the steady flow model and solute transport model to simulate the groundwater flow field and contaminant migration process in groundwater. Before and after the remediation, the pollutant concentrations of Fe and Mn changed significantly, with the maximum concentration of Fe decreasing from 0.351 mg/L to 0.011 mg/L before remediation, and the maximum concentration of Mn decreasing from 0.239 mg/L to 0.007 mg/L, which complied with the groundwater standards, respectively. By modeling contaminant removal under eight scenarios, the results showed that the coupled remediation technology increased the removal rate by 3.96 to 4.99 times compared to the single PRB remediation technology. The removal efficiency reached up to 80.25% in all scenarios. Therefore, the coupled remediation technology has significant effect in groundwater remediation of contaminated sites and provides effective technical support for practical application.