This paper proposes a novel model to optimize the first train timetables for urban rail transit networks, with the goal of maximizing passengers’ transfer waiting time satisfaction. To build up the relationship of transfer waiting time and passenger satisfaction, a reference-based piecewise function is formulated with the consideration of passengers’ expectations, tolerances and dissatisfaction on “just miss”. In order to determine the parameters of zero waiting satisfaction rating, the most comfortable waiting time, and the maximum tolerable waiting time in time satisfaction function, a stated preference survey is conducted in rail transit transfer stations in Shanghai. An artificial bee colony algorithm is developed to solve the timetabling model. Through a real-world case study on Shanghai’s urban rail transit network and comparison with the results of minimizing the total transfer time, we demonstrate that our approach performs better in decreasing extremely long wait and “just miss” events and increasing the number of passengers with a relatively comfortable waiting time in [31s, 5min). Finally, four practical suggestions are proposed for urban rail transit network operations.