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Abstract Background HIIT has recently been widely used for health promotion in healthy people and patients with chronic diseases. Exercise can help SUD reduce drug cravings, enhance mental health and return to normal life. However, whether HIIT can bring better physical rehabilitation benefits to individuals with SUD than MICT is unclear. The study aimed to compare the effects of HIIT versus MICT on the physical fitness of individuals with SUD. Methods One hundred twenty individuals with amphetamine-type stimulant dependence voluntarily participated in this study. They were randomly assigned to the HIIT group and MICT group. Both groups received training three times a week. The intervention lasted from January 2019 to December 2019. Physical fitness was assessed at the baseline, 3 months, 6 months, 9 months and 12 months, including blood pressure (BP), vital capacity(VC), hand grip, push-up, sit-and-reach, one-leg standing with eyes closed and choice reaction time. The craving level was assessed using the Visual Analog Scale at baseline, 6 months and 12 months to see any change along with the improvement in physical fitness. Two-way repeated measures ANOVA was applied to analyse the differences in change by group (HIIT and MICT) and time (baseline, 3 months, 6 months, 9 months and 12 months). Results The within-group factor displayed significant changes in the HIIT and MICT groups in terms of systolic BP (F (4,336) = 12.799, P |