In order to optimize the local search efficiency of multi-objective parameters of flux switching permanent motor based on traditional NSGA-II algorithm, an improved NSGA-II (iNSGA-II) algorithm is proposed, with an anti-redundant mutation operator and forward comparison operation designed for quick identification of non-dominated individuals. In the initial stage of the iNSGA-II algorithm, half of the individual populations were randomly generated, while the other half was generated according to feature distribution information. Taking the flux switching permanent motor stator/rotor gap, permanent magnets width, stator tooth width, rotor tooth width and other parameters as optimization variables, the flux switching permanent motor maximum output shaft torque and minimum torque ripple are taken as optimization objectives, thus a multi-objective optimization model is established. Real number coding was adopted for obtaining the Pareto optimal solution of flux switching permanent motor structure parameters. The results showed that the iNSGA-II algorithm is better than the traditional NSGA-II on convergence. A 1.8L TOYOTA PRIUS model was selected as the prototype vehicle. By using the optimized parameters, a joint optimization simulation model was established by calling ADVISOR’s back-office function. The simulation results showed that the entire vehicle’s 100-km acceleration time is under 8 s and the battery’s SOC value maintains at 0.5–0.7 in the entire cycle, implying that the iNSGA-II algorithm optimizes the flux switching permanent motor design and is suitable for the initial design and optimizing calculation of the flux switching permanent motor.