Background: Chronic chlorella intake combined with high-intensity intermittent training (HIIT) has been shown to accelerate aerobic and anaerobic capacities in rodents. This study aimed to clarify the effects of combining chlorella intake with short-term HIIT on exercise performance in humans, and to investigate the impact of chlorella intake on cardiac adaptation. Materials and Methods: In Study 1, twelve healthy young men completed a 3-week exhaustive HIIT, comprising 6–7 bouts of 20 s of cycling on a leg ergometer at an intensity of 170% maximal oxygen uptake ($\dot{\mathrm{V}}$O_2max), with a 10 s rest between each bout, 3 days/week. They were orally administered either placebo or chlorella during the 3 weeks in a double-blinded, randomized crossover trial (RCT). In Study 2, six healthy young men were orally administered either placebo or chlorella during 4 weeks in a double-blinded, placebo-controlled RCT. We measured $\dot{\mathrm{V}}$O_2max and cardiac function (stroke volume [SV], heart rate [HR], and cardiac output [CO]) during maximal exercise. In Study 3, chlorella-induced changes in molecular markers of maladaptation of the heart were measured in healthy rats. Results: [Study 1] After each HIIT, $\dot{\mathrm{V}}$O_2max significantly increased in the placebo and chlorella groups (p < 0.05). Changes in $\dot{\mathrm{V}}$O_2max were significantly higher in the chlorella group than in the placebo group (p < 0.05). [Study 2] Changes in SV and CO during maximal exercise were significantly higher in the chlorella group than in the placebo group (p < 0.05 each), but HR_max did not change. [Study 3] Chronic chlorella intake did not change the molecular markers of pathological cardiac hypertrophy. Conclusions: Chronic chlorella intake, which improves aerobic capacity by enhancing cardiac function without causing cardiac maladaptation, combined with short-term HIIT, further enhanced aerobic capacity. Thus, the chlorella-induced increase in cardiac function may further enhance aerobic capacity through HIIT.