Abstract: The mechanical properties of the material from the surface of the rail decarburization layer to the substrate exhibit strong non-uniform characteristics, which have a significant impact on the rolling contact between the wheel and the rail. Thusly, a three-dimensional transient rolling contact finite element model of high-speed wheel-rail, which considers the characteristics of the decarburization layer on the steel rail, was established using ANSYS/LS-DYNA, and the influence of the decarburization layer on the wheel-rail contact behavior was analyzed. The non-uniformity of material elastic modulus and hardness of the decarburization layer were obtained through nanoindentation tests. The elastic modulus and hardness gradually decrease from the rail bulk to the surface of the decarburization layer, with the surface elastic modulus and hardness of the decarburization layer decreased by 10% and 34%, compared to the rail bulk. The wheel-rail contact state of the decarburized and non-decarburized steel rail was calculated and compared. It was found that the decarburization layer has a negligible effect on the contact patch size, on the adhesive region distribution and, on the normal contact stress, but has a significant impact on the equivalent stress and strain, as well as the frictional work. After considering the influence of the decarburization layer, the maximum equivalent stress decreased by 20%, and the maximum equivalent strain increased by 115%. Despite the decarburization depth being only 0.55 mm, its impact on the V-M equivalent stress depth reached 3.56 mm.