As stereoscopic three-dimensional (3D) content has gained much popularity, the depth perception of viewers has become an important field of research. However, the relationship between 3D depth parameters and users’ perceptual characteristics has not yet been sufficiently investigated. In this study, we performed psychophysical experiments to investigate changes in the depth perception in relation to pupil distance (PD), 3D display type, viewing distance, and stimuli position. Our research is novel in the following three ways. First, we found that the disparity required for stereoscopic vision increased with the PD, and every increase of 1 mm in the PD value required an additional disparity (contents disparity) of 0.369 mm (1.39 pixels) to perceive the optimal 3D depth. Second, the polarizing filter method required more disparity than the method using shutter glasses. Finally, to provide 3D content with optimal stereoscopic depth, we demonstrated that different functional values, such as PD and 3D display type, should be considered.