This paper develops a framework to conduct a counterfactual analysis to regulate matching markets with regional constraints that impose lower and upper bounds on the number of matches in each region. Our work is motivated by the Japan Residency Matching Program, in which the policymaker wants to guarantee the least number of doctors working in rural regions to achieve the minimum standard of service. Among the multiple possible policies that satisfy such constraints, a policymaker wants to choose the best. To this end, we develop a discrete choice model approach that estimates the utility functions of agents from observed data and predicts agents' behavior under different counterfactual policies. Our framework also allows the policymaker to design the welfare-maximizing tax scheme, which outperforms the policy currently used in practice. Furthermore, a numerical experiment illustrates how our method works.