Sea cucumber (Apostichopus japonicus) is one of the most valuable aquaculture species in China and diseases limit the development of its culture industry. Recently, a novel disease, named body vesicular syndrome (BVS), has been frequently observed during the aquaculture of A. japonicus. Due to it can only found after boiling at the post-harvest process, BVS could result in more severe economic losses than other diseases. In the present study, a multi-mics method covering gut microbiota, pond environmental microbiome, and A. japonicus itself was establish for investigating the BVS. Detailed analyses of differentially expressed proteins and metabolites revealed that the changes of cell adhesion structure caused by disorder of fatty acid beta oxidation mediated by vitamin B5 deficiency might be the main mechanism of BVS occurrence. Furthermore, intestinal dysbacteriosis due to the variation of microbiome in pond water was considered to be the potential reason for vitamin B5 deficiency. A BVS index based on the biomarkers recognized from gut microbiota of A. japonicus was proven to be used for BVS diagnosis. Finally, vitamin B5 supplementation verified the deduced mechanism of BVS and proved that it can be used to treat BVS.