Reducing the number of transfers and improving the operating speed are key factors in enhancing the competitiveness of urban rail transit (URT) systems. This paper proposes an integrated optimization with tactical cross-line planning and an operational express train mode to fully utilize line capacities and reduce the total trip time without additional operating costs and investments. In this paper, a new mixed integer non-linear programming (MINLP) model is proposed for systemically exploring the benefits of cross-line express trains to achieve both passenger travel time and operation cost savings; in this model, the frequencies, stopping patterns and operation zones of cross-line express trains and local trains are simultaneously optimized. The characteristics of same-line trips (SLT) and cross-line trips (CLT) under various stopping patterns are investigated. Additionally, a genetic algorithm (GA) is developed based on the MINLP model. Finally, the effectiveness of the proposed model and heuristic algorithm is verified through a set of real-life instances based on the Beijing URT network. The results show that the number of transfers can be reduced by 78%, with a 3.34% savings of travel time and a 4.66% savings of operating costs, when the cross-line express operating mode is properly adjusted.