New visualization approaches are being actively developed aiming to mitigate the effect of vergence-accommodation conflict in stereoscopic augmented reality; however, high interindividual variability in spatial performance makes it difficult to predict user gain. To address this issue, we investigated the effects of consistent and inconsistent binocular and focus cues on perceptual matching in the stereoscopic environment of augmented reality using a head-mounted display that was driven in multifocal and single focal plane modes. Participants matched the distance of a real object with images projected at three viewing distances, concordant with the display focal planes when driven in the multifocal mode. As a result, consistency of depth cues facilitated faster perceptual judgments on spatial relations. Moreover, the individuals with mild binocular and accommodative disorders benefited from the visualization of information on the focal planes corresponding to image planes more than individuals with normal vision, which was reflected in performance accuracy. Because symptoms and complaints may be absent when the functionality of the sensorimotor system is reduced, the results indicate the need for a detailed assessment of visual functions in research on spatial performance. This study highlights that the development of a visualization system that reduces visual stress and improves user performance should be a priority for the successful implementation of augmented reality displays.