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In order to rationally formulate a customized bus route plan to improve the operation efficiency of customized buses, in view of the problem of ignoring the distance between the boarding area and the alighting area, and setting it as a fixed value when performing custom bus route optimization modeling, as well as solving the problem of multiple custom bus parking lots. This paper proposes a method based on the NSGA-II algorithm using a three-stage hybrid coding method to solve. First, according to real life, the entire operation process of customized buses is divided into four phases. Second, based on the four stages, a multi-objective optimization model of customized bus routes that satisfies multiple parking lots, multiple cars, and multiple boarding and alighting stations is constructed to pursue the minimum total travel time of passengers and minimizes the operating costs of customized bus companies. Third, the NSGA-II algorithm is employed to solve the model, including three-stage hybrid coding, segmented crossover, and segmented mutation operators. Finally, the local road network in Lanzhou City is adopted for simulation research. The results show that it is feasible to use NSGA-II algorithm to solve the problem of customizing bus routes for multiple parking lots, multiple vehicles, and multiple boarding and alighting stations. The research results are of great value for exploring the optimization methods of customized bus routes and improving the operating efficiency of custom buses. [ABSTRACT FROM AUTHOR]