Due to the advantages of high efficiency, zero emission and good drivability, the battery electric vehicles (BEVs) promise to be one of the best choices to replace the oil fueled vehicle. In this paper a solution for the development of a control system for AMT (Automatic Mechanical Trans-mission) equipped in battery electric bus is presented. The system is based on multi-layered architecture that includes two high-level layers and further subdivided into some low-lever layers. The standardized applications interfaces (API) are employed to implement the interlayer interaction. The modular design approach is used during the development process. The system is developed by C language and MATLAB/Simulink/Stateflow toolset and uses Real-Time Workshop tool to generated ANSI C source code. The system is reusable, extensible, and flexible. It is applied in the buses and on-road tests show its correctness, efficiency, reliability.