Aiming at an electric mini commercial vehicle developed for facing the European market, the side pole impact simulation test was carried out according to the E-NCAP regulation. The results show that the side wall of the vehicle and the side wall of the power battery pack at the bottom are seriously deformed. By analyzing the energy transfer path of the body-in-white, the thickness of seven main components such as B-pillar and threshold beam was selected as the design variable. Taking the lightweight of the vehicle and the improvement of collision energy absorption as the optimization objectives, the response surface approximation model was constructed, and the multi-objective optimization was carried out in combination with newly proposed MOMSA. After optimization, the energy absorption of the relevant component structure is increased by 22.3%, and the mass is reduced by 2.1%. At the same time, in the side column collision, the intrusion of the abdomen and the lower threshold of the B column is reduced by 22.5% and 26.3% respectively. However, the deformation of the bottom structure of the body is still large and the deformation of the battery pack accounted for about 12.4% of the overall size, and the safety of the battery pack still has hidden dangers. Therefore, lotus root bionic thin-walled energy absorption structure is filled in the longitudinal beam on the right side of the battery pack. It is found that the side wall of the battery pack is only slightly deformed after re-collision after filling, and the deformation is less than 10% of the overall size, which meets the safety requirements. Through multi-objective optimization and filling of bionic thin-walled energy-absorbing structure, the overall improvement of occupant and battery safety performance of the target vehicle under side pole impact conditions is finally achieved.