Purpose This study aimed to investigate the effects of 4-week continuous hypoxic training (CHT) on skeletal muscle oxygenation and hemodynamics, assessed using functional near-infrared spectroscopy (NIRS) and blood oxygenation level-dependent functional magnetic resonance imaging (fMRI-BOLD). Methods Twenty-six healthy male participants were randomly assigned to CHT group (FiO₂ = 14.8–15.3%) or a normoxic training (CON) group (FiO₂ = 20.3–20.8%). Participants underwent a 4-week supervised treadmill endurance training program at their ventilatory anaerobic threshold. Assessments included that muscle oxygen saturation (SmO₂) measurements using NIRS during graded exercise, and fMRI-BOLD imaging during ischemia–reperfusion to evaluate skeletal muscle perfusion and oxygenation in pre- and post-intervention. Results Significant increases were observed in SmO₂ at 20% (68.43 ± 5.90 vs 62.53 ± 6.70), 40% (64.50 ± 7.46 vs 55.20 ± 7.43), 60% (54.42 ± 3.71 vs 45.63 ± 5.99), 80% (45.97 ± 5.91 vs 41.18 ± 6.40), and 100% (36.04 ± 6.62 vs 27.57 ± 5.66) exercise intensities (p textless 0.046) in CHT group as compared to CON group. Additionally, PHV (p textless 0.011), MIV (p textless 0.003), TTP (p = 0.024), THIM (p textless 0.045), and TTR (p textless 0.003) were significantly improved after 4-week CHT intervention as compared to normoxic training, suggesting enhanced vascular reactivity and oxygen utilization efficiency. Conclusion These findings demonstrate that CHT may enhance skeletal muscle oxygenation and perfusion, suggesting potential utility in endurance training and rehabilitation intervention by improving skeletal muscle oxygenation and perfusion, as evidenced by increased SmO₂ and enhanced BOLD responses, suggesting potential utility in endurance training and rehabilitation contexts. The application of fMRI-BOLD and NIRS provides novel insights into microvascular adaptations.