As excessive crossed disparity is known to cause visual discomfort, this study aims to establish a classification model to discriminate excessive crossed disparity in stereoscopic viewing in combination with subjective assessment of visual discomfort. A stereo-visual evoked potentials (VEPs) experimental system was built up to obtain the VEPs evoked by stereoscopic stimulus with different disparities. Ten volunteers participated in this experiment, and forty VEP datasets in total were extracted when the viewers were under comfortable viewing conditions. Six features of VEPs from three electrodes at the occipital lobe were chosen, and the classification was established using the Fisher's linear discriminant (FLD). Based on FLD results, the correct rate for determining the excessive crossed disparity was 70%, and it reached 80% for other stimuli. The study demonstrated cost-effective discriminant classification modelling to distinguish the stimulus with excessive crossed disparity which inclines to cause visual discomfort.