The traditional steel structure has many disadvantages, including excessive mass and high density. Owing to the characteristics of low density, high strength-to-weight ratio and excellent energy absorption, metallic sandwich structures with cellular core have attracted tremendous attention in recent years and become significant protective structure in transportation industry, aerospace structures and marine structures fields. The design of the core layer plays an important role in damping and noise reduction of the overall structure, and the panel thickness variation of the structure also has an important effect. In this paper, the effects of core density and panel thickness are considered. The configuration of three-layer hourglass lattice sandwich structure is designed. The relative density of each core layer is changed with sectional dimension of core truss members to establish four gradient models; three thickness ratios are employed for the front and rear panels of four gradient models in order to compare when keeping the total thickness of the front and rear panels of the model constant. The commercial software ABAQUS was used to simulate the vibration of 12 models to obtain the first to tenth natural frequencies of each model, and the results were compared to probe the influence of core density and thickness ratio of the front and rear panels on overall structural vibration.