Based on analysis results of the character and mechanism of subgrade disease, the dynamic behavior of new typesubgrade with semi-rigid water-proof structure layer was researched. Due to the effects of semi-rigid waterproof structure, the dynamic response of new type cutting bedding was different from the traditional with train loads. In this article effect of the semi-rigid waterproof structure thickness on dynamic response of cutting bedding was been researched. The resultsshow that, with the increase of the waterproof structure thickness, the dynamic stress in bedding changes little, the dynamic displacement of subgrade surface decreases linearly.