The BCI system based on Steady-Stated Visual Evoked Potential (SSVEP) is used widely because of its high system stability, information transfer rate (ITR), and accuracy. Accuracy is an important indicator to evaluate the BCI system performance. There has been a lot of research on the effect of the SSVEP paradigm parameters, such as frequency, shape, color, etc., on recognition accuracy. In this paper, we focus on the influence of the layout of different frequencies on the performance of BCI systems. We carried out experimental verification in the SSVEP-based BCI system. The experimental results show that adjusting the frequency layout improves the recognition accuracy of the system from 93.61% to 96.11%.