Recently, SSVEP(steady-state visual evoked potential-based BCI(brain-computer interface) researches have achieved significant development. However, the practical application of BCIs are still limited by several factors, one of which is the visual stimulus source. Most SSVEP-BCI systems rely on monitors, which are not portable and thus restrict the practical use in daily life. VR glasses, as wearable and portable devices, can provide realistic and immersive stimulus sources, which do not rely on monitors. Thus, they offer significant potentials for BCI applications. The VR(virtual reality) technology was introduced to display VR-SSVEP visual stimuli in 3D environment and enables subjects to immersively engage in BCI. The performance of 3D and 2D visual stimuli based on VR-SSVEP were compared in this study. The experimental results demonstrate that the performance of 3D visual stimuli is better than that of 2D visual stimuli. The average classification accuracy of 3D stimuli reaches 90.10%, which is 7.08% higher than 2D stimuli. Additionally, a 2-second stimulation duration achieves an optimal information transfer rate. This study confirms that 3D visual stimuli can effectively enhance SSVEP recognition performance, which indicates a practical use of the system and provides a novel approach for applying VR devices to the SSVEP paradigm.