Our previous study established an asynchronous BCI system by using the oddball paradigm to simultaneously induce event-related potentials (ERPs) and visual evoked potentials (VEPs) (E-V BCIs). We found that stimulus onset asynchrony (SOA) is an important factor for performance since it significantly affects the ERP and VEP. Increasing the SOA increases the ERP, which improves the accuracy of detecting target stimuli. However, a larger SOA leads to a lower VEP frequency, which causes the VEP to have poor accuracy when discriminating between the brain states. How to balance the two potentials and accuracies is a problem. This study established eight SOAs from 100 ms to 375 ms that were composed of different interstimulus intervals and the same stimulus duration of 80 ms. We used a probability-based Fisher linear discriminant analysis (P-FLDA) classifier to calculate the classification accuracies of the ERP-based visual speller, VEP-based brain state discrimination, and E-V BCI. The results show that as the SOA increases, the amplitudes of N200 and P300 increase, and the accuracy also shows an increasing trend. However, the frequency of the VEP and the accuracies of state discrimination show downward trends. The change in accuracies of the E-V BCI system combining these two parts is nonlinear, and the SOA optimal value is 125 ms. The SOA of 125 ms yields the best accuracies of 95.83% and practical bit rate of 57.17 bits/min in the E-V BCI system, which provides a guideline for selecting the SOA to improve the performance.