Recent advances in holographic displays include increased interest in multiplexing techniques, which allow for extension of viewing angle, hologram resolution increase, or color imaging. In each of these situations, the image is obtained by a composition of a several light wavefronts and therefore some wavefront misalignment occurs. In this work we present a calibration method, that allows for correction of these misalignments by a suitable numerical manipulation of holographic data. For this purpose, we have developed an automated procedure that is based on a measurement of positions of reconstructed synthetic hologram of a target object with focus at two different reconstruction distances. In view of relatively long reconstruction distances in holographic displays, we focus on angular deviations of light beams, which result in a noticeable mutual lateral shift and inclination of the component images in space. A method proposed in this work is implemented in a color holographic display unit (single Spatial Light Modulator – SLM) utilizing Space- Division Method (SDM). In this technique, also referred as Aperture Field Division (AFD) method, a significant wavefront inclination is introduced by a color filter glass mosaic plate (mask) placed in front of the SLM. It is verified that an accuracy of the calibration method, obtained for reconstruction distance 700mm, is 34.5 μm and 0.02°, for the lateral shift and for the angular compensation, respectively. In the final experiment the presented method is verified through real-world object color image reconstruction.