There are two modes to display panoramic movies in virtual reality (VR) environment: non-stereoscopic mode (2D) and stereoscopic mode (3D). It has not been fully studied whether there are differences in the activation effect between these two continuous display modes on emotional arousal and what characteristics of the related neural activity are. In this paper, we designed a cognitive psychology experiment in order to compare the effects of VR-2D and VR-3D on emotional arousal by analyzing synchronously collected scalp electroencephalogram signals. We used support vector machine (SVM) to verify the neurophysiological differences between the two modes in VR environment. The results showed that compared with VR-2D films, VR-3D films evoked significantly higher electroencephalogram (EEG) power (mainly reflected in α and β activities). The significantly improved β wave power in VR-3D mode showed that 3D vision brought more intense cortical activity, which might lead to higher arousal. At the same time, the more intense α activity in the occipital region of the brain also suggested that VR-3D films might cause higher visual fatigue. By the means of neurocinematics, this paper demonstrates that EEG activity can well reflect the effects of different vision modes on the characteristics of the viewers’ neural activities. The current study provides theoretical support not only for the future exploration of the image language under the VR perspective, but for future VR film shooting methods and human emotion research.