This study investigated how Jerusalem artichoke powder (JAP) affected the growth, immunity, and gut microbiota of the sea cucumber, Apostichopus japonicus Selenka. Animals were fed diets containing antibiotic (1 ppm) or five levels of JAP (0, 2.5, 5, 10, and 15 g/kg). After the feeding trial, three sea cucumbers were sampled per tank to assay for immunity and gut microbiota composition. Dietary supplementation of 2.5 g/kg JAP significantly improved the growth rate and phenoloxidase activity of sea cucumbers. The diet containing 5 g/kg of JAP increased the survival rate and phagocytic activity, and the diet containing 15 g/kg of JAP increased the growth rate and total coelomocyte count of sea cucumbers. Moreover, exposure to antibiotics significantly changed the microbiota of sea cucumbers, while the JAP supplementation stimulated the development of microbiota communities, which could be more homogeneous. Supplementing the diets with 15 g/kg of JAP increased the growth of Rhodobacterales, and this may underlie the higher growth rate of sea cucumbers in this treatment. Considered together, our results suggest that supplementing the diet of sea cucumber with JAP may be beneficial for nonantibiotic farming of sea cucumber.