The eigenvibration properties of honeycomb sandwich panels are investigated in this paper. A new numerical modeling for eigenvibration analysis of the honeycomb sandwich panels is proposed under the assumption that the orthotropic shell and two kinds of beam elements represent face materials, adhesive layers and honeycomb core, respectively. The shell element is also connected to the beam element through the thickness. The effects of geometry of honeycomb core and thickness of face material on the eigenfrequency are examined through the comparisons between finite element simulation and experimental results. It is shown as a result that the eigenvibration properties depend strongly on the face material rigidity and honeycomb core geometry. The implications of the findings for the design of eigenvibration of honeycomb sandwich panels are discussed from the point of view of overall flexural rigidity.