A 60 d feeding experiment was conducted to investigate the effects of oxidized fish oil (OF) on survival, growth, immune and antioxidant capacity, inflammation-related gene expression, and intestinal microbiota of juvenile sea urchin (Strongylocentrotus intermedius). Six feeds were formulated by including equal amounts of fish oil with different oxidation levels (0, 50, 100, 150, 200, and 300 meq/kg). The feed OF0 and fresh kelp (Laminaria japonica) were used as the control groups. Results showed that the weight gain rate (WGR) of sea urchins significantly decreased as the oxidation level increased. When the oxidation level of fish oil was equal to or above 150 meq/kg, the WGR of sea urchins was significantly lower than those fed the control diets. The activities of digestive enzymes (pepsin and amylase), immune enzymes (alkaline phosphatase and acid phosphatase), and antioxidant enzymes (superoxide dismutase, catalase, and glutathione S-transferase) first decreased significantly as the oxidation level increased to 150 or 200 meq/kg and then bounced to values comparable to or even higher than those in the control feed group, while the transcription of immune, antioxidation, and inflammation-related genes was upregulated by the increasing oxidation level of fish oil. Oxidized fish oil decreased the intestinal microbial diversity and the relative abundance of Firmicutes. Vibrio was the dominant genus of microbiota in the intestine of sea urchins fed almost all formulated feeds (except for OF150), with its abundance above 20%. Comparably, the abundance of Vibrio in the intestine of sea urchins fed fresh kelp was only 2.32%. These results showed that oxidized fish oil had negative effects on the growth, immune response and antioxidant capacity, and bacterial diversity of juvenile S. intermedius. The abnormal increase of antioxidant enzyme activities and malondialdehyde contents at relatively higher oxidation level (>150 meq/kg) could be due to the oxidative stress occurrence inside the body of sea urchins. Sea urchins fed formulated feeds host more Vibrio than those fed fresh kelp, and this could be a potential incidence of disease occurrence.