Public transportation is a crucial component of urban transportation systems, and improving passenger sharing rates can help alleviate traffic congestion. To enhance the punctuality and supply–demand balance of dedicated buses, we propose a hierarchical multi-objective optimization model to optimize bus guidance speeds and bus operation schedules. Firstly, we present an intelligent decision-making method for bus driving speed based on the mathematical description of bus operation states and the application of the Lagrange multiplier method, which improves the overall punctuality rate of the bus line. Secondly, we propose an optimization method for bus operation schedules that respond to passenger needs by optimizing departure time intervals and station schedules for supply–demand balance. The experiments were conducted in Future Science City, Beijing, China. The results show that the bus line’s punctuality rate has increased to 90.53%, while the retention rate for platform passengers and the intersection stop rate have decreased by 36.22% and 60.93%, respectively. These findings verify the effectiveness and practicality of the proposed hierarchical multi-objective optimization model.