People with overweight or obesity preferred high-intensity interval training (HIIT) due to the time-efficiency and pleasure. However, HIIT leads to delayed onset muscle soreness (DOMS). The present study aimed to investigate the effects of omega-3 supplementation on DOMS, muscle damage, and acute inflammatory markers induced by cycling HIIT in untrained males with overweight or obesity. A randomized, double-blinded study was used in the present study. Twenty-four males with a sedentary lifestyle were randomly assigned to either receive omega-3 (O3) (4 g fish oil) or placebo (Con). Subjects consumed the capsules for 4 weeks and performed cycling HIIT at the 4th week. After 4 weeks-intervention, the omega-3 index of O3 group increased by 52.51% compared to the baseline. All subjects performed HIIT at 4th week. The plasma creatine kinase (CK) level of Con group increased throughout 48h after HIIT. While the CK level of O3 group increased only immediately and 24h after HIIT and decreased at 48h after HIIT. The white blood cell count (WBC) of Con group increased immediately after the HIIT, while O3 group did not show such increase. There was no change of CRP in both groups. O3 group had a higher reduction of calf pain score compared to Con group. O3 group also showed a recovery of leg strength faster than Con group. Omega-3 supplementation for 4 weeks lower increased CK level, reduced calf pain score, and recovery leg strength, DOMS markers after cycling HIIT.