Crack defects may appear at the raceway surface of the cylindrical roller bearings (CRBs) due to bearing overload, fatigue, and poor lubrication conditions. The emergence of raceway crack defects can reduce the contact stiffness between the bearing raceway and the roller, which is a key excitation mode for roller bearing vibration. An accurate contact stiffness modeling method considering the raceway crack defects can provide guidance for the establishment of the roller bearing dynamic model and its fault diagnosis. When a roller passes through a defective raceway, the stiffness of contact that occurs between the roller and the raceway changes, causing vibrational impacts during bearing operation, and then affecting the bearing service performance. This paper introduces a new methodology for calculating the contact stiffness between the roller and the raceway with a non-through crack defect in a roller bearing, relying on the finite element (FE) method and the classical Hertzian contact theory. In this method, the contact region where the raceway and the roller meet in the axial direction is divided into two parts according to whether the raceway has defects. The first part is referred to as the normal contact area, and the second part is the defective contact area. The contact stiffness belonging to the normal contact area is able to be calculated using classical Hertzian contact theory. However, the stiffness of the defective contact area cannot be directly solved using Hertzian contact theory, as it includes both contact deformation and structural deformation at the contact position. The total stiffness of the defective contact area is a series connection of those two stiffness values. It can be considered that the contact of the roller with the defective raceway is a plane strain problem. A FE equivalent model of this contact is established to calculate its structural stiffness. Therefore, the total stiffness of the contact occurring between the raceway and the roller containing the non-through crack defect is the parallel connection of those two stiffness values of the above-mentioned two parts. The research findings indicate that when a roller passes through a non-through raceway crack defect area, the contact stiffness from the raceway to the roller decreases. Besides, the crack depth and the crack inclination angle can also affect the stiffness in the contact area.