Abstract The skip-stop operation strategy (SOS) is rarely applied to Chinese urban rail transit networks because it is a simple scheme and a less universally popular transportation service. However, the SOS has performance advantages, in that the total trip time can be reduced depending on the number of skipped stations, crowds of passengers can be rapidly evacuated at congested stations in peak periods, and the cost to transit companies is reduced. There is a contradiction between reducing the trip time under the SOS and increasing the passengers’ waiting times under an all-stop scheme. Given this situation, the three objectives of our study were to minimize the waiting and trip times of all passengers and the travel times of trains. A comprehensive estimation model is presented for the SOS. The mechanism through which the trip time for all passengers is affected by the SOS is analyzed in detail. A 0-1 integer programming formulation is established for the three objectives, and is solved using a tabu search algorithm. Finally, an example is presented to demonstrate that the estimation method for the SOS is capable of optimizing the timetable and operation schemes for a Chinese urban rail transit network.