Brain-computer interface based on steady-state visual evoked potential has been widely studied due to the high information transfer rate, little user training, and wide subject applicability. However, there are also disadvantages such as visual discomfort and “BCI illiteracy.” To address these problems, this study proposes to use low-frequency stimulations, which can simultaneously elicit visual evoked potential and pupillary response to construct a hybrid BCI system. Classification accuracy was calculated using supervised and unsupervised methods, respectively, and the hybrid accuracy was obtained (...) using a decision fusion method to combine the information of VEP and PR. Online experimental results from 10 subjects showed that the averaged accuracy was 94.90 ± 2.34% for the supervised method and 91.88 ± 3.68% for the unsupervised method, which correspond to the ITR of 64.35 ± 3.07 bits/min and 33.19 ± 2.38 bpm, respectively. Notably, the hybrid method achieved higher accuracy and ITR than that of VEP and PR for most subjects, especially for the short data length. Together with the subjects’ feedback on user experience, these results indicate that the proposed h-BCI with the low-frequency stimulation paradigm is more comfortable and favorable than the traditional SSVEP-BCI paradigm using the alpha frequency range. (shrink)