Intestine regeneration in the sea cucumber Apostichopus japonicus is a fascinating biological event and a typical example for studying host-intestinal microbiota interactions. The intestinal microbiota may play important roles in developing intestine promotion, but the underlying mechanism remains unclear. Notably, altered microbiota abundance may be a key marker of the observed ecosystem. To understand the role of the developing intestinal microbiota in intestine regeneration via quantitative data, we developed a germ-free sea cucumber model and analyzed the intestinal microbial differentiation of faster and slower regenerating A. japonicus individuals during intestine regeneration. The results revealed that depletion of the intestinal microbiota resulted in elevated abundance of the potential key players Flavobacteriaceae and Rhodobacterales during intestine regeneration and thus promoted the intestine regeneration rate of A. japonicus. These results first revealed a direct link between intestinal microbial quantity and microbiome features and the intestinal regrowth rate of A. japonicus. Metagenomic analysis revealed that the increased abundance of Flavobacteriaceae elevated the enrichment of genes associated with carbohydrate utilization, whereas the abundant Rhodobacteraceae -enriched genes were associated with polyhydroxybutyrate production. We identified microbiota abundance as a key driver of microbial community alterations, especially beneficial microbiota members, in the developing intestine of A. japonicus. This study provides new insights into the mechanism of host-microbiota interactions related to intestine development, and the understanding of molecular diversity to questions within intestinal ecology.