Steady-state visual evoked potential brain-computer interfaces (SSVEP-BCI) have attracted significant attention due to their ease of deployment and high performance in terms of information transfer rate (ITR) and accuracy, making them a promising candidate for integration with consumer electronics devices. However, as SSVEP characteristics are directly associated with visual stimulus attributes, the influence of stereoscopic vision on SSVEP as a critical visual attribute has yet to be fully explored. Meanwhile, the promising combination of virtual reality (VR) devices and BCI applications is hampered by the significant disparity between VR environments and traditional 2D displays. This is not only due to the fact that screen-based SSVEP generally operates under static, stable conditions with simple and unvaried visual stimuli but also because conventional luminance-modulated stimuli can quickly induce visual fatigue. This study attempts to address these research gaps by designing SSVEP paradigms with stereo-related attributes and conducting a comparative analysis with the traditional 2D planar paradigm under the same VR environment. This study proposed two new paradigms: the 3D paradigm and the 3D-Blink paradigm. The 3D paradigm induces SSVEP by modulating the luminance of spherical targets, while the 3D-Blink paradigm employs modulation of the spheres' opacity instead. The results of offline 4-object selection experiments showed that the accuracy of 3D and 2D paradigm was 85.67 and 86.17% with canonical correlation analysis (CCA) and 86.17 and 91.73% with filter bank canonical correlation analysis (FBCCA), which is consistent with the reduction in the signal-to-noise ratio (SNR) of SSVEP harmonics for the 3D paradigm observed in the frequency-domain analysis. The 3D-Blink paradigm achieved 75.00% of detection accuracy and 27.02 bits/min of ITR with 0.8 seconds of stimulus time and task-related component analysis (TRCA) algorithm, demonstrating its effectiveness. These findings demonstrate that the 3D and 3D-Blink paradigms supported by VR can achieve improved user comfort and satisfactory performance, while further algorithmic optimization and feature analysis are required for the stereo-related paradigms. In conclusion, this study contributes to a deeper understanding of the impact of binocular stereoscopic vision mechanisms on SSVEP paradigms and promotes the application of SSVEP-BCI in diverse VR environments.