To optimize the protective design of logistics packaging for Hami melons, a sweep frequency vibration test was conducted on the 5-layer stacked packaging of Hami melons. The collected vibration signals were analyzed using the DASP V11 software to obtain the natural frequencies, peak acceleration, and vibration transmission rates of the middle and side parts of the packaging in each stacking layer. Polynomial regression models of the relationship between peak acceleration, maximum vibration transfer rate and stacking layer were established respectively. The test results show that the peak acceleration and the maximum vibration transmission rate of the same stacking layer in the middle of the package are both greater than those in the side. The peak acceleration and maximum vibration transfer rate of each stacking layer show an increasing trend from the bottom layer to the top layer. The peak acceleration and the maximum vibration transfer rate both show a significant positive correlation with the stacking layer. Therefore, when optimizing the protection design of package parts, considerations should be given to optimizing the cushioning design in the middle of the package and at the top of the packages.