To investigate whether high-intensity interval training (HIIT) and continuous moderate-intensity training (CMT) have different impacts on exercise performance and cardiac function and to determine the influence of these exercise protocols on modulating basal autophagy in the cardiac muscle of rats. Rats were assigned to three groups: sedentary control (SC), CMT, and HIIT. Total exercise volume and mean intensity were matched between the two protocols. After a 10-week training program, rats were evaluated for exercise performance, including exercise tolerance and grip strength. Blood lactate levels were measured after an incremental exercise test. Cardiac function and morphology were assessed by echocardiography. Western blotting was used to evaluate the expression of autophagy and mitochondrial markers. Transmission electron microscopy was used to evaluate mitochondrial content. The results showed that time to exhaustion and grip strength increased significantly in the HIIT group compared with the SC and CMT groups. Both training interventions significantly increased time to exhaustion, reduced blood lactate level (after an incremental exercise test) and induced adaptive changes in cardiac morphology, but without altering cardiac systolic function. The greater improvements in exercise performance with the HIIT than with the CMT protocol were related to improvement in basal autophagic adaptation and mitochondria function in cardiac muscle. Mitochondria markers were positively correlated with autophagy makers. This study shows that HIIT is more effective for improving exercise performance than CMT and this improvement is related to mitochondrial function and basal autophagic adaptation in cardiac muscle.