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In code-modulated visual evoked potential (c-VEP) based BCI systems, flickering visual stimuli may result in visual fatigue. Thus, we introduced a discrete-interval binary sequence (DIBS) as visual stimulus modulation, with its power spectrum optimized to emphasize high-frequency components (40 Hz-60 Hz). 8 and 17 subjects participated, respectively, in offline and online experiments on a 4-target asynchronous c-VEP-based BCI system designed to realize a high positive predictive value (PPV), a low false positive rate (FPR) during idle states, and a high true positive rate (TPR) in control states, while minimizing visual fatigue level. Two visual stimuli modulations were introduced and compared: a maximum length sequence (m-sequence) and the high-frequency discrete-interval binary sequence (DIBS). The decoding algorithm was compared among the canonical correlation analysis (CCA), the task-related component analysis (TRCA), and two approaches of sub-band component weight calculation (the traditional method and the proportional method) for FBCCA and FBTRCA. In the online experiments, the average PPV, FPR and TPR achieved, respectively [Formula: see text], [Formula: see text], [Formula: see text] with m-sequence, while [Formula: see text], [Formula: see text] and [Formula: see text] with DIBS. Estimated by objective eye-related metrics and a subjective questionnaire, the visual fatigue in DIBS cases is significantly smaller than that in m-sequence cases. In this study, the feasibility of a novel modulation approach for visual fatigue reduction was proved in an asynchronous c-VEP system, while maintaining comparable performance to existing methods, which provides further insights towards enhancing this field's long-term viability and user-friendliness.