In brain function measurements by near-infrared spectroscopy, improving the measurement accuracy and expanding the measurement region are important for analyzing brain functional connectivity. Furthermore, for improvement of measurement accuracy, it is necessary to detect a signal for correcting disturbances or changes in skin blood flow. We have proposed a multi-channel signal processing method for realization of disturbance cancelation. To implement the cancelation method in an equilateral triangular probe placement, it is necessary to irradiate from each vertex sequentially and detect the light at the other vertices and at the center of the triangle. Thus, we adopt a combination of the multiple pulse method and the digital encoding method. Computer simulations show that treating the digital code in a pseudo-analog manner is effective for reducing the external noise and preventing mistakes in the demodulation bits. The demodulation process is confirmed using a phantom experiment and is then applied to the cancelation method. Using the cancelation method, the influence of a near-surface absorber is reduced from 64% to 27%. Thus, the multi-channel signal processing that we developed for the cancelation method improves measurement accuracy without increasing the system size.