Massive harmful algal blooms (HABs) have increased the risk of marine organisms encountering the dinoflagellate toxin, okadaic acid (OA). Strongylocentrotus intermedius, a globally significant benthic aquaculture species, has a large appetite for benthic algae. During red tide events, there is a high risk of red tide toxin accumulation. This study systematically evaluated the potential impact of short-term OA exposure on the behavior and physiological functions of juvenile S. intermedius. From typical (5 μg/L) to extreme OA concentrations (20 μg/L) during HAB outbreaks, OA exposure gradually inhibited a series of tube foot-related behaviors (sheltering, foraging, righting, and tube-foot tenacity). At OA concentrations during HAB outbreaks (5 μg/L), the tube foot function of S. intermedius was progressively inhibited. Further physiological indicator analyses revealed that the activity of antioxidants increased over a short period to prevent damage from reactive oxygen species induced by OA. However, OA ultimately suppressed the immune response of S. intermedius, leading to apoptosis. Although HAB-associated concentrations of OA (5 μg/L) did not induce a continuous increase in the integrated biological response index of S. intermedius, this study speculated that HABs pose a future risk to echinoderm species. Notably, principal component analysis results showed that OA exposure eventually induced significant changes in the production of O2-, malondialdehyde, and total glutathione, as well as in glutathione S-transferase activity and caspase-7, -8, and -9 levels. This study provides preliminary evidence of OA’s toxic effects on sea urchins and essential data for urgent risk assessments of algal toxin pollution in aquaculture during HABs.