A 8‐week feeding trial was conducted to evaluate the effects of combined oral administration of the yeast Rhodotorula sp. H26 and bacterium Bacillus sp. BC26 on growth, digestive enzyme activity, body composition, immunity, and intestinal microbiota in the juvenile sea cucumber, Apostichopus japonicus. Sea cucumbers were divided into four groups and received one of the following diets: BD) basal diet; H) H26; B) BC26; HB) H26 + BC26. After feeding for 4 and/or 8 weeks, sea cucumbers fed the HB diet showed a significant increase in specific growth rate, pepsin, trypsin, amylase, and lipase activities, and body wall crude protein, carbohydrate, arachidonic and adrenic acids contents compared with the BD and/or single probiont (H26 and/or BC26) groups. Feeding the mixture significantly improved phagocytic activity and respiratory burst of the coelomocytes, and lysozyme activity and phenoloxidase activity of the coelomic fluid supernatant and coelomocyte lysate supernatant compared with the BD and and/or single probiont (H26 and/or BC26) groups. Gel electrophoresis revealed that the mixture of H26 and BC26 did not significantly affect the composition of intestinal microbiota. These data suggest that a mixture of H26 and BC26 supplementation can improve the growth, enhance digestive enzyme activity, add nutritional value, and stimulate the innate immune system of sea cucumber juveniles.