The work aims to study the finite element simulation analysis method for vibration transmissibility of honeycomb paperboard with different structural and material parameters, with respect to the vibration protection performance of honeycomb paperboard. Based on the finite element software Abaqus/Standard, the honeycomb paperboard-mass system model was established. Then, two kinds of honeycomb paperboards were set up with different liner material parameters and honeycomb cell side length. The vibration transmissibility of honeycomb paperboards was analyzed by simulation and verified by experiments. The vibration transmissibility-frequency curve of honeycomb paperboard was obtained through simulation and experiment. The error between the simulation result of resonance frequency and the experimental value was less than 3.43%, and the error between the simulation result of vibration transmissibility and the experimental value during resonance was less than 11.31%. The finite element simulation method can be used to obtain the vibration transmissibility of honeycomb paperboard with different structural and material parameters. Moreover, the simulation analysis results show that the effect of liner grammage on vibration transmissibility of honeycomb paperboard is small, while the resonance frequency of system of honeycomb paperboard with larger honeycomb cell length is smaller, yet the change of vibration transmissibility is not obvious.