Laying insulation material is an effectively method to deal with the frost damages. In the engineering practice, the insulation material will be exposed to water and freezing-thawing cycles (FTC), and its thermal performance may be change. To clarify the effect of FTC on the thermal conductivity, after the polyurethane (PU) board suffered from different numbers of FTC, both the water absorption and the thermal conductivity were measured, and a correction coefficient was introduced to reduce the difference between the measured and designed thermal conductivities. Besides, the selection of the correction coefficient was illustrated by the designing the insulation layer. The results show that (1) after 300 numbers of FTC, the water absorption can reach 34.5% and the thermal conductivity increases to 0.042 W/(m.K), which are 18.5 times and 1.7 times of those before FTC, respectively. (2) The correction coefficients of the PU board vary from 1.065 to 1.701, the water can amplify the influence of FTC on the correction coefficient. (3) For the Lehua tunnel, it is recommended to increase the insulation layer thickness to 5.50 cm, which is fixed at the surface of the secondary lining. The results can not only help us to understand the deterioration of PU board caused by FTC, but also provide a guideline for designing the insulation layer with the correction of thermal conductivity.