Abstarct: Background: Obesity is associated with impaired cellular homeostasis, chronic inflammation, and dysregulation of autophagy pathways, all of which contribute to the development of mextabolic disorders. Exercise training is recognized as an effective non-pharmacological strategy for improving mextabolic health; however, the effects of different exercise intensities on autophagy biomarkers remain unclear. Therefore, this study aimed to investigate the effects of eight weeks of exercise training with different intensities on autophagy indices in inactive obese men. Methods: This semi-experimental study employed a pretest–posttest design with a control group. Thirty inactive obese men aged 30–40 years were randomly assigned to three groups: Moderate-Intensity Training (MIT), High-Intensity Training (HIT), and a control group (n = 10 per group). The intervention lasted eight weeks with three exercise sessions per week. The MIT group performed aerobic exercise at 50–65% of heart rate reserve (HRR), whereas the HIT group performed interval training at 80–90% of maximal heart rate (HRmax). Blood samples were collected before and after the intervention, and the autophagy biomarkers LC3-II and Beclin-1 were measured using ELISA. Data were analyzed using one-way ANOVA followed by Tukey's post hoc test, with statistical significance set at P < 0.05. Results: Both exercise protocols significantly reduced the serum levels of LC3-II and Beclin-1 compared with the control group (P < 0.05). The MIT group demonstrated the greatest reduction in LC3-II, whereas the HIT group exhibited the greatest reduction in Beclin-1. Significant differences were observed among the three groups for both biomarkers, indicating that exercise intensity influences autophagy responses. Conclusion: Both moderate- and high-intensity exercise training effectively improved autophagy-related biomarkers in inactive obese men. However, exercise intensity differentially affected the autophagy response, with moderate-intensity exercise producing greater reductions in LC3-II and high-intensity exercise exerting a stronger effect on Beclin-1. These findings suggest that selecting an appropriate exercise intensity may represent an effective strategy for improving obesity-related mextabolic dysfunction.