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Abstract Background Discomfort evoked by stereoscopic depth has been widely concerned. Previous studies have proposed a comfortable disparity range and considered that disparities exceed this range would cause visual discomfort. Brain activity recordings including Electroencephalograph (EEG) monitoring enable better understanding of perceptual and cognitive processes related to stereo depth-induced visual comfort. Methods EEG data was collected using a stereo-visual evoked potential (VEP) test system by providing visual stimulus to subjects aged from 21 to 25 with normal stereoscopic vision. For each type of visual stimulus, data were processed using directed transfer function (DTF) and adaptive directed transfer function (ADTF) in combination with subjective feedbacks (comfort or discomfort). The topographies of information flow were constructed to compare responses stimulated by different stereoscopic depth, and to determine the difference in comfort and discomfort situations upon stimulation with same stereoscopic depth. Results Based on EEG analysis results, we found that the occipital P270 was moderately related to the disparity. Moreover, the ADTF of P270 showed that the information flows at frontal lobe and central-parietal lobe changed when stimulation with different stereoscopic depth applied. As to the stereo images with same stereoscopic depth, the DTF outflows at the temporal and temporal-parietal lobes in δ band, central and central-parietal lobes in α and θ bands, and the comparison of inflows in these three bands could be considered as discriminated indexes for matching the stereoscopic effect with viewers’ comfort or discomfort state impacted by disparity. The subjective feedbacks indicated that the comfort judgments remained as a result of cumulative effect. Conclusions This study proposed a short-term stereo-VEP experiment that shorted the duration of each stimulus in the experimental scheme to minimize the interference from other factors except the disparity. The occipital P270 had a mid-relevance to the disparity and its ADTF showed the affected areas when viewers are receiving stimulations with different disparities. DTF could be considered as discriminated indexes for matching the stereoscopic effect with viewers’ comfort or discomfort state induced by disparity. This study proposed a preferable experiment to observe the single effect of disparity and provided an intuitive and easy-to-read result in a more convenient manner.