Polymers exposed to tritiated water undergo hydrogen defects caused by isotope substitution and subsequent β-decay of substituted tritium, causing structural changes and loss of function in the biopolymers. Here, based on linear response theory, we predict the structural change of tritium-damaged polyethylene using the equilibrium trajectory of undamaged polyethylene to reduce the computation time of molecular dynamics simulations. Specifically, the ensemble average of the change in a physical quantity, such that it represents a structural change before and after damage, was calculated numerically using the time derivative of the total potential energy difference derived analytically and the physical quantity obtained from the simulation of undamaged polyethylene on the basis of linear response theory. A comparison between theoretical and simulation results revealed that the characteristic oscillation behaviors of the structural response of polyethylene can be predicted, whereas the quantitative prediction of the steady-state values over a long period is difficult.