This study aims to design a steady state visual evoked potentials (SSVEP) based brain-computer interface (BCI) system with only three electrodes. It is known that low frequency flickering induces more intensive SSVEP, but might cause users feel uncomfortable and easily tired. Therefore, this paper proposes a novel middle/high frequency flickering stimulus. However, users show different SSVEP responses when gazing at the same stimuli. It is improper to design fixed frequency flickering stimuli for all users. This study firstly proposes a strategy to adjust the stimuli frequency for each user that could cause better SSVEP. Moreover, to further enhance the SSVEP, this study incorporates flickering duty-cycle for stimuli design, which has been discussed less for SSVEP-based BCI systems. The proposed system consists of two modes, flicker frequency/duty-cycle selection mode and application mode. The flicker frequency/duty-cycle selection mode obtains two best frequencies between 24 and 36 Hz with their related optimal duty-cycle. Then the system goes into the application mode to control the devices. A new fact that has been found is that the optimal flicker frequency and duty-cycle do not vary with time. It means once the optical flicker frequency and duty-cycle is determined the first time, flicker frequency/duty-cycle selection mode does not need to operate the next time. Furthermore, the phase coding technology is used to extend the one command/one frequency to multi command/one frequency. Experimental results show the proposed system has good performance with average accuracy 95% and average command transfer interval 4.4925 s per command.