Background: High-intensity Interval Training (HIIT) has recently been widely used for health promotion in healthy people and patients with chronic diseases. It is not clear whether HIIT can bring better physical rehabilitation benefits to individuals with substance use disorder (SUD) than that of Moderate-intensity continuous Training (MICT). The study aimed to compare the effects of HIIT versus MICT on the physical fitness of individuals with SUD.Methods: A total 120 individuals with amphetamine-type stimulant dependent from a compulsory drug rehabilitation center voluntarily took part in this study. They were randomly assigned to the HIIT group (experimental group) and MICT group (control group). The subjects in experimental group received HIIT training three times a week (80%-85%HRMax, 60min). The exercise included rope jumping, running, weight training and basketball game. The subjects from control group received MICT 3 times a week (60%HRMax, 60min), including Tai Chi, mind-body exercise and recreation activity. Physical fitness assessment were performed at the baseline, 3 months, 6 months, 9 months and 12 months exercise intervention including blood pressure (BP), vital capacity (VC), hand grip, push-up, sit-and-reach, one-leg-stand with eyes closed and choice reaction time. The craving level was assessed using the visual analog scale (VAS)at the baseline, 6 months and 12 months. A two-way repeated measures analysis of variance (ANOVA) was applied to test whether the intervention were different after 12 months.Results: The within-group factor displayed significant changes in HIIT and MICT groups in terms of the systolic BP (F (4,336) =12.799), diastolic BP (F(4,336) =9.495), VC (F(4,336)=18.121), hand grip (F(4,336)=34.815), sit-and-reach (F(4,336) =13.871), choice reaction time (F(4,336) =20.603), one-leg-stand with eyes closed (F(4,336) =14.495) and push-up (F(4,336) =28.805). The craving level decreased after 12 months intervention in both groups (F(2,168) =11.25, P<0.001), but there was not significant differences between HIIT and MICT group.Conclusion: Both HIIT and MICT can promote the physical fitness rehabilitation for individuals with SUD. Clinical Trials Registry: ChiCTR1900022158 Chinese Clinical Trial Registry