We investigated how the mechanism for perceiving motion-in-depth based on interocular velocity differences (IOVDs) integrates signals from the motion spatial frequency (SF) channels. We focused on the question whether this integration is implemented before or after the comparison of the velocity signals from the two eyes. We measured spatial frequency selectivity of the MAE of motion in depth (3D MAE). The 3D MAE showed little spatial frequency selectivity, whereas the 2D lateral MAE showed clear spatial frequency selectivity in the same condition. This indicates that the outputs of the monocular motion SF channels are combined before analyzing the IOVD. The presumption was confirmed by the disappearance of the 3D MAE after exposure to superimposed gratings with different spatial frequencies moving in opposite directions. The direction of the 2D MAE depended on the test spatial frequency in the same condition. These results suggest that the IOVD is calculated at a relatively later stage of the motion analysis, and that some monocular information is preserved even after the integration of the motion SF channel outputs.