Previous research comparing traditional two-dimensional (2D) and virtual reality with stereoscopic vision (VR-3D) stimulations revealed that VR-3D resulted in higher levels of immersion. However, the effects of these two visual modes on emotional stimulus processing have not been thoroughly investigated, and the underlying neural processing mechanisms remain unclear. Thus, this paper introduced a cognitive psychological experiment that was conducted to investigate how these two visual modes influence emotional processing. To reduce fatigue, participants (n = 16) were randomly assigned to watch a series of 2D and VR-3D short emotional videos for two days. During their participation, electroencephalograms (EEG) were recorded simultaneously. The results showed that even in the absence of sound, visual stimuli in the VR environment significantly increased emotional arousal, especially in the frontal region, parietal region, temporal region, and occipital region. On this basis, visual evoked potential (VEP) analysis was performed. VR stimulation compared to 2D led to a larger P1 component amplitude, while VEP analysis based on the time course of the late event-related potential component revealed that, after 1200 ms, the differences across visual modes became stable and significant. Furthermore, the results also confirmed that VEP in the early stages is more sensitive to emotions and presumably there are corresponding emotion regulation mechanisms in the late stages.