The customized bus (CB) is an innovative type of transit service that can provide a personalized efficient transit services for passengers and environmental friendliness and congestion alleviation in metropolitan areas. This work develops an integrated optimization method for CB stop deployment, route design, and timetable development optimization problems while meeting travel demands as much as possible to obtain system-optimal CB service plans. Through the perspective of space-time network, the CB service design problem (CBSDP) is formulated as an integrated optimization model with the objectives of maximizing passenger accessibility and minimizing operating cost. An inconvenience index of passengers is introduced in the problem to measure the service quality, and the total number of stops for all involved CB routes is set as one of the objectives to optimize the total cost of the CB system. A heuristic approach is applied to generate efficient solutions for the CBSDP. Two types of instance, namely, a numerical experiment and a real-world instance, are implemented to demonstrate the performance of the proposed method. We also conduct a series of sensitive analyses to explore the influences of various parameters on the CB system for capturing the interaction among stops, routes, and timetables. Final results show that the CB plans obtained by the proposed method can provide efficient services by balancing passenger convenience and operating cost.