Abstract Pareto optimization solves a constrained optimization task by reformulating the task as a bi-objective problem. Pareto optimization has been shown quite effective in applications; however, it has little theoretical support. This work theoretically compares Pareto optimization with a penalty approach, which is a common method transforming a constrained optimization into an unconstrained optimization. We prove that on two large classes of constrained Boolean optimization problems, minimum matroid optimization (P-solvable) and minimum cost coverage (NP-hard), Pareto optimization is more efficient than the penalty function method for obtaining the optimal and approximate solutions, respectively. Furthermore, on a minimum cost coverage instance, we also show the advantage of Pareto optimization over a greedy algorithm.