Vibration is one of the most common loading modes during handling and transport of solar silicon wafers and has a great influence on the breakage rate. In order to control the breakage rate during handling and facilitate the optimization of the processing steps, it is important to understand the factors which influence the natural frequency of thin silicon wafers. In this study, we applied nonlinear finite element method to investigate the correlation of natural frequency of thin solar silicon wafer with material microstructures (grain size and grain orientation), thickness variation and crack geometry (position and size). It has been found that the natural frequency for anisotropic single crystal silicon wafer is a strong function of material orientation. Less than 10% thickness variation will have a negligible effect on natural frequency. It is also found out that cracks smaller than 20 mm have no dominant effect on the first five natural frequency modes anywhere in the silicon wafer.