Honeycomb is a splendid kind of structure for aerospace engineering with the advantages of light weight, good shock absorption, and good structural stability. This article aims to provide methods to isolate Pyroshocks based on a honeycomb structure and guarantee the safety of such equipment against a high-frequency shock response. According to stress wave theory, an equation for stress wave transmittance of the honeycomb structure is derived considering the effect of cell wall length and thickness, where desirable honeycomb parameters are obtained. The complexity of the transfer path of the honeycomb structure is exploited to build the spacecraft–rocket interface, which could increase the impedance of the stress wave dramatically. Both finite element analysis and experiments are carried out to validate the shock isolation strategies. The influence of parameters, such as cell wall length and the thickness of the stainless-steel honeycomb, on the isolation performance is analyzed. It is revealed that the honeycomb structure has a significant effect on Pyroshock isolation performance when the wall length of the honeycomb cell is 8 mm and the thickness of the cell is 0.1 mm.