Photoplethysmography (PPG) is an easy and convenient method by which to measure heart rate (HR). However, PPG signals that optically measure volumetric changes in blood are not robust to motion artifacts. In this paper, we develop a PPG measuring system based on multi-channel sensors with multiple wavelengths and propose a motion artifact reduction algorithm using independent component analysis (ICA). We also propose a truncated singular value decomposition for 12-channel PPG signals, which contain direction and depth information measured using the developed multi-channel PPG measurement system. The performance of the proposed method is evaluated against the R-peaks of an electrocardiogram in terms of sensitivity (Se), positive predictive value (PPV), and failed detection rate (FDR). The experimental results show that Se, PPV, and FDR were 99%, 99.55%, and 0.45% for walking, 96.28%, 99.24%, and 0.77% for fast walking, and 82.49%, 99.83%, and 0.17% for running, respectively. The evaluation shows that the proposed method is effective in reducing errors in HR estimation from PPG signals with motion artifacts in intensive motion situations such as fast walking and running.