As a new public transport service mode, customized bus (CB) can meet the diversified and personalized travel needs of residents. However, it is difficult for bus operators to make precise customizations. In this paper, considering the characteristic of variable CB stations and passenger demand, a mixed integer programming model is developed for the CB bus route design, and a two-stage heuristic with CW saving algorithm and variable neighborhood search is proposed. The proposed methodology is validated using a real-world transit network in Beijing. The results show that the occupancy rates of the most CB bus lines designed in this paper can reach 100%, and the average occupancy rate can reach 91.67%.