Previous studies have suggested that virtual reality (VR) can elicit emotions in different visual modes using 2D or 3D headsets. However, the effects on emotional arousal by using these two visual modes have not been comprehensively investigated, and the underlying neural mechanisms are not yet clear. This paper presents a cognitive psychological experiment that was conducted to analyze how these two visual modes impact emotional arousal. Forty volunteers were recruited and were randomly assigned to two groups. They were asked to watch a series of positive, neutral and negative short VR videos in 2D and 3D. Multichannel electroencephalograms (EEG) and skin conductance responses (SCR) were recorded simultaneously during their participation. The results indicated that emotional stimulation was more intense in the 3D environment due to the improved perception of the environment; greater emotional arousal was generated; and higher beta (21-30 Hz) EEG power was identified in 3D than in 2D. We also found that both hemispheres were involved in stereo vision processing and that brain lateralization existed in the processing.