In depth cue-conflict conditions, various depth cues could represent different extents of depth. Previous studies have investigated the perceived size of negative afterimage in depth cue-correlated conditions in which different cues introduce almost the same amounts of depth to the visual system. This study examined the perceived size of the afterimage in the human observers in a condition that depth cues of texture gradient, linear perspective and gradient of disparity entered into a conflict with cues of absolute binocular disparity, accommodation and convergence. On a 2-D flat screen, a picture of a room that had two cubes inside was shown to seven observers. They were asked to fixate their gaze on the center of a red circle, which was shown randomly on the front surface of one of these cubes for 50 seconds. Observers then should shift their gaze toward the front surface of the other cube and report perceived size of afterimage by adjusting the size of an adjustable blue ring. The result of this experiment shows that the perceived afterimage size has significant difference with adaptation stimulus size. Note that a control experiment has done and its result confirms the above-mentioned finding. Considering that neural correlates of texture gradient, linear perspective and gradient of disparity are located in higher level visual area than neural correlate of absolute binocular disparity, our results point out that in this cue-conflict condition, the afterimage size is determined mainly by higher level depth cues and therefore, consistent with modified weak fusion theory (MWF), in the depth cue averaging procedure, these higher level cues have more weight than other cues that are processed in lower level visual areas.