A comprehensive contact analysis model to determine the contact positions and clearances of mating thread surfaces in the planetary roller screw mechanism (PRSM) is proposed in this paper. By introducing a three-dimensional clearance vector, the modified conditions of continuous tangency of mating surfaces are established, in which the clearances along all the directions and contact positions of an arbitrary pair of mating surfaces can be calculated. The deviations of the screw, roller, and nut from their nominal positions are considered in the transformation matrices, which describe the position relations of the screw, roller, and nut. Then, the equations of thread surfaces with deviations are derived. Using the modified conditions and the equations of surfaces, the meshing equations at the screw–roller and nut–roller interfaces are derived to compute the clearances along all the directions and contact positions of mating thread surfaces on each pair of thread teeth in the imperfect PRSM. The effectiveness of the proposed model is verified by comparing the contact positions at the screw–roller interface with those from the previously published model. Then, the effect of the direction of clearance vector on the clearances and contact positions is analyzed and discussed. Because of the roller deviation, the clearances between multiple pairs of thread teeth are no longer identical, and the contact positions of a pair of mating thread surfaces on different pairs of thread teeth are different. Also, the parameters of a PRSM without clearances can be obtained from the proposed model in the design process.