As the subway system is beginning to operate interval trains in the early morning, it is necessary to discuss the first train timetable synchronization with interval trains. In this paper, with the consideration of both ordinary trains and interval trains, we study the first train timetable problem with minimum total transfer waiting time. The first train timetable model is formulated as a mixed integer programming problem and a genetic simulated annealing algorithm is developed to deal with the case study of Beijing subway network. The proposed model and the algorithm are effective in improving the performance of the first train timetable synchronization. After optimization, the total transfer waiting time and the number of long waiting time transfer directions for Beijing subway network have decreased significantly. The results indicate that operating interval trains is an effective way to solve the problem of long waiting time in early morning.