This work focuses on investigating the optimal design of composite sandwich plates (FCSPs) with a viscoelastic square honeycomb core (VSHC). Firstly, using the cross-fill theory, the complex modulus technique, the first-order shear deformation theory, the minimum strain energy principle, and the Newmark-β method, a theoretical model of the VSHC-FCSPs under half-sine pulse excitation is formulated to calculate the inherent frequencies, the peak and vibration decay time of the transient response in time domain. The peak and vibration decay time are taken as the indexes of the anti-vibration performance. Considering an index of structural stiffness performance, the average value of the inherent frequencies is adopted to calculate the overall stiffness. After a set of literature validations and optimization validations, the multi-objective genetic algorithm is employed to study the optimization issue of VSHC-FCSPs. The optimization objectives are to minimize the three design variables of the transient response peak, vibration decay time, and reciprocal of overall stiffness. Then, the fiber laying angle of each layer, the core thickness ratio and the modulus ratio are assumed as optimization variables. Finally, the results with good vibration resistance and structural stiffness in the Pareto front are chosen as references, and these corresponding variations of the design variables and optimization objectives are obtained. The optimization results have revealed that the optimization variables corresponding to the intermediate points should be selected as references to improve the anti-vibration capacity and ensure the structural stiffness performance.