In this paper, we present a multi-objective simulation-based headway optimization for complex urban mass rapid transit systems. Real-world applications often confront conflicting goals of cost versus service level. We propose a two-phase algorithm that combines the single-objective covariance matrix adaptation evolution strategy with a problem-specific multi-directional local search. With a computational study, we compare our proposed method against both a multi-objective covariance matrix adaptation evolution strategy and a nondominated sorting genetic algorithm. The integrated discrete event simulation model has several stochastic elements. Fluctuating demand (i.e., creation of passengers) is driven by hourly origin-destination-matrices based on mobile phone and infrared count data. We also consider the passenger distribution along waiting platforms and within vehicles. Our twophase optimization scheme outperforms the comparative approaches, in terms of both spread and the accuracy of the resulting Pareto front approximation.