A linear differential equation is adopted to account for the complexity of honeycomb paperboard properties under static and dynamic conditions. Based on the Laplace transform, honeycomb paperboard is modeled as a linear material with viscoelastic property. The free response of the mass loaded honeycomb paperboard system is expressed as the sum of complex exponentials. The residues and eigenvalues are obtained accurately using the structured nonlinear total least norm(SNTLN) method. A parameters estimation procedure is formulated using a substitution strategy. A experiment system is set up, a series of tests is carried out under different load condition, the free response data of the mass loaded honeycomb paperboard system are recorded and they are used to estimate the parameters. The stiffness coefficients, damping coefficients and viscoelastic coefficients are presented as the function of the load. The model in this work can be used to simulate the response of the mass loaded honeycomb paperboard system under shock condition.