The overlap of bus and rail transit routes is common in China. This overlap provides passengers multiple choices for one trip. However, the availability of multiple options would cause uncertainty in the travel distribution of passengers. Given that buses and rail transits are becoming increasingly common, this paper aims to present the overlapped operation condition of bus and rail transit using a bi-level model from the perspective of bus operators. Frequency optimization model is established in the upper-level model. A heuristic algorithm called shuffled complex evolution (SCE-UA) method is used to solve the established frequency optimization model, and three other heuristic methods are compared with SCE-UA. A lower-level Logit model based on Agent simulation is set for traffic mode split. Data on the transit system in Dalian city are chosen as an example to test the feasibility of the model and the algorithm. Results show that as the overlapped optimization of bus route and rail transit routes changed primary bus frequency, the use of SCE-UA to solve such problems has evident advantages and feasibility; furthermore, changed bus frequency would improve bus operations.