Stereoscopic visual fatigue (SVF) due to prolonged immersion in the virtual environment can lead to negative user experience, thus hindering the development of virtual reality (VR) industry. Previous studies have focused on investigating the evaluation indicators associated with SVF, while few studies have been conducted to reveal the underlying neural mechanism, especially in VR applications. In this paper, a modified Go/NoGo paradigm was adopted to induce SVF in VR environment with Go trials for maintaining participants’ attention and NoGo trials for investigating the neural effects under SVF. Random dot stereograms (RDSs) with 11 disparities were presented to evoke the depth-related visual evoked potentials (DVEPs) during 64-channel EEG recordings. EEG datasets collected from 15 participants in NoGo trials were selected to conduct individual processing and group analysis, in which the characteristics of the DVEPs components for various fatigue degrees were compared and independent components were clustered to explore the original cortex areas related to SVF. Point-by-point permutation statistics revealed that DVEPs sample points from 230 ms to 280 ms (component P2) in most brain areas changed significantly when SVF increased. Additionally, independent component analysis (ICA) identified that component P2 which originated from posterior cingulate cortex and precuneus, was associated statistically with SVF. We believe that SVF is rather a conscious status concerning the changes of self-awareness or self-location awareness than the performance reduction of retinal image processing. Moreover, we suggest that indicators representing higher conscious state may be a better indicator for SVF evaluation in VR environments.