In this work, the influence of vias design on hybrid bonding is explored by finite element analysis approach. The impact of via shape, width, depth, and pad dishing on the bonding quality are firstly investigated by taking the copper pad with one via into account. The results indicate that the bonding quality is determined by the via width, depth, and pad dishing, while the via shape is of little influence. Followingly, the simulation about one via design is extended to the via array design. An optimized via array arrangement is achieved with a high contact area ratio and uniform interfacial stress at last. The simulation results in this paper are expected to provide guidelines for optimizing the hybrid bonding process.