The medical facility location problem has attracted increasing attention in recent years because the rational layout of medical facilities plays an important role in implementing the hierarchical diagnosis and treatment system in many countries. To promote the implementation of a hierarchical diagnosis and treatment system, a two-level medical facility location problem with multiple patient flows between demand points and medical facilities is studied in this paper. We use a direct interpretation of the two-level medical facility location problem as a multi-objective problem to effectively balance different conflicting objectives. Based on the multi-objective tabu search algorithm and the fast construction method of the Pareto non-dominated solution, we also propose a solution approach to yield a set of solutions that can represent the trade-offs among conflicting objectives. The applicability and validation of the presented model and performance of the proposed optimization approach are evaluated using a real case. The experimental results not only indicate that the proposed solution approach can effectively solve the two-level medical facility location problem, but also suggest that the presented model can provide significant results in determining locations for medical facilities.