This study investigated the effectiveness of using a high-density multi-distance source-detector (SD) separations in near-infrared spectroscopy (NIRS), for enhancing the performance of a functional NIRS (fNIRS)-based brain-computer interface (BCI). The NIRS system that was used for the experiment was capable of measuring signals from four SD separations: 15, 21.2, 30, and 33.5 mm, and this allowed the measurement of hemodynamic response alterations at various depths. Fifteen participants were asked to perform mental arithmetic and word chain tasks, to induce task-related hemodynamic response variations, or they were asked to stay relaxed to acquire a baseline signal. To evaluate the degree of BCI performance enhancement by high-density channel configuration, the classification accuracy obtained using a typical low-density lattice SD arrangement, was compared to that obtained using the high-density SD arrangement, while maintaining the SD separation at 30 mm. The analysis results demonstrated that the use of a high-density channel configuration did not result in a noticeable enhancement of classification accuracy. However, the combination of hemodynamic variations, measured by two multi-distance SD separations, resulted in the significant enhancement of overall classification accuracy. The results of this study indicated that the use of high-density multi-distance SD separations can likely provide a new method for enhancing the performance of an fNIRS-BCI.