The purpose of this study was to elucidate the time course of muscle deoxygenation and its heterogeneity changes through endurance training. Nine healthy untrained male participated in this study. The subjects performed a ramp incremental cycle exercise protocol to estimate VO2peak and muscle tissue oxygen saturation (SmO2) distribution in the VL muscle before and after 3 (3 wk-T) and 6 weeks of endurance training (6 wk-T). The probe of multi-channel near infrared spatially resolved spectroscopy was attached to the left vastus lateralis muscle along the direction of the long axis. The subjects performed cycle exercise at 60 % of VO2peak for 30 min/day, 3 days/week as the endurance training. After the training, VO2peak at 3 wk-T and 6 wk-T were significantly increased compared to pre-training (Pre-T) and VO2peak at 6 wk-T was significantly increased compared to 3 wk-T. Mean SmO2 within measurement sites at VO2peak was significantly decreased after 3 wk-T and 6 wk-T compared to Pre-T, but mean SmO2 was not significantly different between 3 wk-T and 6 wk-T. Conversely, the heterogeneity of the SmO2 during exercise was not significantly changed through endurance training. A significantly negative correlation was found between ΔVO2 and ΔSmO2 after the first 3 weeks of endurance training. In contrast, no correlation was found between ΔVO2 and ΔSmO2 after the last 3 weeks of endurance training. These results suggest that the enhanced muscle O2 availability may be one of the primary factors in increasing VO2peak after the first 3 weeks of endurance training.