As the key airborne system of electric vertical takeoff and landing (eVTOL) aircraft, flight control system needs to have the same safety requirement as civil aircraft. In order to design the flight control system architecture to meet the requirements of eVTOL aircraft, redundancy design technology of the flight control computer, sensor and actuator for eVTOL aircraft flight control system was introduced and an eVTOL aircraft flight control system architecture was designed based on the safety requirements according to airworthiness regulations. The typical functional hazards under the rotor configuration of eVTOL aircraft were analyzed, and the safety analysis was carried out by using the fault tree analysis technology. The results show that the typical functional hazards of the flight control system architecture designed in this study can meet the requirements of failure probability.