Skin ulceration syndrome is among the most harmful diseases in sea cucumber (Apostichopus japonicus). The annual loss due to this disease is more than 1 billion dollars, which seriously affected the healthy and sustainable development of A. japonicus. In this paper, animals were divided into 4 experimental groups: a control group given basic feed, experimental groups with 1% Lactobacillus, 1% Bacillus, 1% mixture with 0.5% Lactobacillus and 0.5% Bacillus added to the basic feed. After feeding for 60 days, the samples were taken to analyze the growth performance, digestive enzyme activity, and immune indexes of A. japonicus. Furthermore, the resistance to the skin ulceration syndrome of A. japonicus was analyzed. The results showed that the probiotics promoted the growth performance of A. japonicus, the weight gain rate of the control group was 120.08±12.07%, the weight gain rate of the Lactobacillus group was 152.11±10.06%, the weight gain rate of the Bacillus group was 148.03±9.88%, and the weight gain rate of the mixed bacteria group was as high as 210.11±19.41%. The digestive enzyme activities in the intestinal tract of A. japonicus increased significantly in the probiotic-added groups, and the mixed bacteria were more effective in enhancing the digestive enzyme activities than single Bacillus and Lactobacillus. In addition, the probiotics could significantly increase the phagocytosis rate of the body cavity cells of A. japonicus. The phagocytic rate of Lactobacillus and Bacillus subtilis was comparable; the mixed probiotics were significantly higher than those of single probiotics, and this phagocytic rate gradually increased over time. After Vibrio splendidus and Pseudoalteromonas infection, the mortality rate of A. japonicus in the probiotic-added group was reduced, which indicated that probiotics could improve the immunity of A. japonicus, and the ability to resist the infection of Vibrio splendidus and Pseudoalteromonas was enhanced. Bacillus exhibits superior antimicrobial ability compared to Lactobacillus, and the mixed strain displays the most effective antimicrobial properties. This study provided a scientific basis for effectively preventing and controlling skin ulceration syndrome in the aquaculture of A. japonicus.