Multilayer stacked corrugated packaging boxes are a common shipping mode in packaging distribution. This study discusses how to determine the damping properties of stacked corrugated boxes using experimental modal analysis (EMA). Prior to the calculation of damping properties, two MATLAB-based digital filters were applied to process the sampled original signals. Both the logarithmic method and the curve fit method are used to compute the multiple damping ratios from the acceleration and displacement response data after the excitation. The study found that the viscous damping and dry friction damping take place in a different time frame in stacked corrugated boxes. This study recommends using the curve fit method to determine damping properties for a multiple-degree-of-freedom system such as stacked corrugated boxes.