In order to investigate the effect of bulk substrate deformation on the micro contact characteristics of joint surfaces in mixed lubrication, a contact stiffness model of joint surfaces considering bulk substrate deformation is proposed. Firstly, the asperity contact stiffness and bulk substrate contact stiffness are obtained by the single asperity-bulk substrate system model, and the contact deformation of asperity is determined by the fixed point iteration method. Then, the normal contact stiffness model of the solid surface is established based on fractal theory with considering bulk substrate deformation. Furthermore, the solid contact stiffness is used to obtain liquid contact stiffness model. The results show that the normal load from the proposed model is smaller than the model that ignores bulk substrate deformation, when the real contact area is constant. Meanwhile, the contact stiffness of joint surfaces is mainly dominated by liquid contact stiffness in the early stage of contact. However, the ratio of the liquid contact stiffness to the total stiffness decreases with increasing the real contact area. Finally, the solid contact stiffness dominates joint surfaces. This model provides a theoretical basis for studying the contact characteristics of joint surfaces in mixed lubrication.