Permanent magnet synchronous motors (PMSM) are widely used in the electric vehicles for their high power density and high energy efficiency. And the motor control system for PMSMs is one of the most safety critical systems in electric vehicles, because potential failures in this system can lead to serious harm to the human’s body, so normally a high automotive safety integrity level (ASIL) will be assigned to this system. In this paper, an ASIL-C motor control system based on a multicore micro-controller is presented. Meanwhile, since there are more and more connectivities available on the vehicle, secure onboard communication conformed to the AUTOSAR standard is also implemented in the system to prevent external attack. In this paper, the functional safety development process of the system is presented: first the system is defined according to its functionalities and interfaces, and then the hazard analysis and risk assessment of the system is carried out and the safety goals are derived. A proposed system design based on the E-GAS 3-layer architecture and technical safety requirements are given in the system design phase. For system design verification the failure mode and effect analysis (FMEA) and fault tree analysis (FTA) are introduced. Software architecture is developed based on the automotive open system architecture (AUTOSAR) and the model based design (MBD) method is used for the application layer software. And secure onboard communication usage is also described in the paper to a mechanism to authenticate and verify the CAN messages between the vehicle control unit and the motor control system.