At present, the optimization of public transportation networks and vehicle scheduling are carried out independently in stages. However, through analysis, it has been found that scheduling information such as route schedules is an important factor related to passenger route selection. Therefore, in order to further improve the optimization effect, this article proposes an innovative idea of simultaneously optimizing the line network and scheduling. Based on the construction of a real–virtual public transportation network, this article constructs a synchronous optimization model for the line network and scheduling by considering both passenger waiting and on-board time. To achieve the consideration of passengers for different route choices, a shortest path traversal algorithm based on Yen was proposed to analyze the number and weight of the shortest paths between the same OD, and a genetic algorithm was used to solve the model. Finally, the effectiveness of the model was verified through numerical examples, and the results showed that synchronous optimization was superior to phased optimization: the passenger time cost was reduced by 21.5%, the bus operation cost was reduced by 13.7%, and the total bus system cost was reduced by 18.0%.