The unstable running time and the difficulty to accurately estimate the arrival time reduce passengers’ satisfaction with bus traveling. With the diversification of cities, bus line types are gradually becoming more diverse, and the variations in bus operating time of the various bus line types cause trouble in bus scheduling and inconvenience for passengers. To solve above problems, firstly, this paper used K-means ++ algorithm to cluster the stations with the sum of squares of error (SSE) as the measurement index. The operation characteristics and reliability influencing factors of different types of bus lines were taken into consideration to determine the alternative station sets of limited-stop bus service. Then, a joint optimization strategy model of limited-stop bus service and speed regulation was proposed to determine the limited-stop bus station, the departure time, and the running speed of all buses. This model took the minimization of bus operation cost, passenger travel cost, and reliability cost as the objectives, and took the constraints of operation process and headway of limited-stop bus service and all-stop bus service into consideration. Finally, genetic algorithm was used to solve the optimization model and Beijing bus system was selected for case analysis. The results show that the limited-stop bus service can reduce the operation cost of public transport, the speed regulation strategy can better lower the passenger travel cost and reliability cost, and the joint optimization strategy of limited-stop bus service and speed regulation can effectively reduce the total cost of the bus system.