A multi-layer software-defined architecture is developed based on a type of elementary power module to improve the energy conversion performance of electric vehicle (EV) system. The proposed structure is composed of three layers: (1) application function layer for the interfaces with various types of electrified loads/sources and the corresponding control functions, such as single/three-phase grid, battery, motor, resistor; (2) elementary module layer for providing desired number of basic power module with local functions of variable frequency soft switching (VFSS) and model predictive control (MPC) to increase the efficiency with better transient performance; (3) interconnection management layer for the coordination and interconnection between the application function layer and elementary module layer to construct the complete power converter topology with desired number of elementary power module for the satisfaction of the interfaced load/source. The merits of the designed architecture include the reconfigurability to be suitable for different types of EV applications, all non-isolated topologies with common mode noise attenuation capability, improved efficiency and dynamic performance by VFSS and MPC of the elementary power module, high accuracy and robustness of the multi-layer control without being influenced by the parametric modeling error from various applications. The proposed multi-layer architecture is validated with experimental tests.