The risk of liquid agitation in pump-driven tanks within integrated tanks has significantly escalated due to the growing demands for tank integration in new-energy vehicles. In order to solve the problem of liquid sloshing in integrated tanks, this paper presents the design of a baffle structure aimed at reducing waves in integrated water tanks. The numerical simulation method of combining the level-set function with the volume of fluid (CLSVOF) has been employed, significantly enhancing the accuracy of numerical calculations related to a two-phase flow field inside an integrated tank. A comparison was made by analyzing different factors, notably baffle length (L), baffle depth (H), and baffle angle (θ), to investigate their influences in suppressing liquid agitation within the integrated water tank. Numerical computations were conducted utilizing design points acquired by the Latin hypercube sampling technique. The Kriging approximation modelling method was employed to hold down computing time. The Pareto solution was obtained by means of the non-dominated sorting genetic algorithm II, while the optimal solution set was evaluated and ranked using the multi-criteria decision-making algorithm (MCDM). The results show that increasing the baffle depth within a certain range can effectively suppress the wave height in the tank. When the baffle depth is increased to a certain value, the effect on wave-height suppression in the water tank is limited. When the baffle length and angle of the baffle exceed a certain value, it will also have the effect of suppressing the wave height in the tank. After comparing various factors of the baffle, it was ultimately found that the wave suppression effect is maximal when the length of the baffle is 13 millimeters, the depth of the baffle is 49 millimeters, and the angle of the baffle is -20 degrees. The main contribution of this study is the proposed wave-suppressing baffle structure, which provides new insights for the future structural design of integrated water tanks.