To solve the problem that the vertical negative effect of electric vehicles (EVs) is aggravated when added with in-wheel motor (IWM), the influence of different suspended configurations of IWM on vehicle vertical performance was studied under the coupling excitations of road excitation and motor vertical excitation. Effects of various configurations of EVs at home and abroad on ride comfort were comprehensively analyzed. The ride comfort of two schemes of IWM stator and whole motor suspended as dynamic absorber of vehicles was compared, and the computational model of dual excitations was built and used to select the optimal scheme. Then, by taking the minimum root mean square (RMS) value of vehicle ride comfort index as the optimization objective, NSGA-II algorithm was applied to optimize the stiffness and damping of rubber bushing of dynamic vibration absorber in the optimal scheme, and suitable configuration and matching parameters were obtained. At last, the optimized vehicle configuration was verified by simulation. Results show that the proposed two suspended schemes both alleviated the negative effects, while after the optimization of the selected whole motor suspended scheme, the acceleration of the vehicle body and the dynamic load of the tyre were reduced by 38.53% and 7.94% respectively. Simulation results verify that the optimized configuration and parameters under dual excitations reduced the vertical negative effect of EV driven by IWM and improved the vehicle ride comfort and safety.