The numerical modeling and modal analysis had been investigated on vibration of magnesium alloy honeycomb panels. With a simplified model of honeycomb panel, imposing the boundary and initial conditions, the distribution of the natural frequency and inherent vibration mode of the honeycomb sample could be simulated by using Lanczos method, the summit amplitudes and the most dangerous points are found. The effective factors such as materials modulus, the density as well as the assembling all contribute to the analyzed results. The vibration modes and the basic vibration frequencies were analyzed. According to the analysis, the risk-reduction program is proposed.