The probiotic effects of Bacillus subtilis E20-supplemented diets (control (without probiotics), 108, 109, and 1010 CFU kg−1, respectively designated Control, E108, E109, and E1010) fed to Oplegnathus fasciatus for 56 days were evaluated by tracking the growth performance, innate immune responses, and disease resistance against Vibrio alginolyticus at low temperature (~ 20 °C). The survival and dorsal muscle compositions of fish among groups after 56 days rearing were no significant differences. The enhancement of growth performance was recorded only in group E108 with limited effects on innate immunity and no alteration of disease resistance against V. alginolyticus in parrot fish. Interestingly, the innate immunity of O. fasciatus was improved with increased probiotics concentration, but the growth performance was suppressed, especially in group E1010. The cumulative mortality against V. alginolyticus was significantly reduced in group E1010 as a result of increase of lysozyme activity, respiratory burst and phagocytic activity except superoxide dismutase activity. Therefore, it is considered that the probiotic, B. subtilis E20 could perform its probiotic efficiency at low temperature, and the diet containing 108 CFU kg−1 of B. subtilis E20 is recommended to improve the growth performance of O. fasciatus.