Due to the high information transfer rate and accuracy, SSVEP-based BCI interfaces are widely used in the engineering field. However, the SSVEP paradigm can induce various symptoms of visual discomfort in users after long-term work because it relies on the user’s continual attention and confirmation towards flickering objects on the interface. To improve this condition, our study organized an simulated typing experiment with 20 subjects to investigate the impact of frequency and size of flickering icons on visual comfort within a BCI interface. Throughout the experimentation process, subjects’ subjective comfort levels and ocular characteristics were monitored to assess their overall comfort. The experimental results showed that both frequency and size significantly affect the visual comfort of subjects when performing BCI tasks. As the frequency range increased, users’ visual comfort ratings were higher, while an increase in size led to the opposite effect. Considering the interaction between these two factors, a icon size smaller than 4 \(^\circ \) and a flickering frequency above 40Hz would yield the optimal visual experience. The findings can be directly applied to optimizing design for SSVEP-based BCI interfaces.