The stimuli color greatly affects the performance of a steady-state visual evoked potential (SSVEP)-based brain computer interface (BCI). However, few studies have evaluated the effect of stimuli color combination on the multiple-target BCI when the stimuli adopt different colors. In this study, 16 sets of colors were tested by using an online dual-task BCI, and the detection accuracy, time and information transmission rate (ITR) were measured. The results showed that the yellow-red combination achieved the highest accuracy, shortest time and highest ITR, which is the optimal choice for improving the performance of BCI.