Abstract: To examine temporal patterns in the intestinal microbiota of juvenile Nibea albiflora, as well as their associations with rearing-water bacterial communities, intestinal contents and corresponding water samples were collected at 36, 46, 66, 86, and 106 days post-hatching. High-throughput 16S rRNA gene sequencing and bioinformatics analyses were used to profile community composition, structure, succession, core taxa, and their relationships with host growth and rearing water microbiota. Across all sampling points, the Chao1 index of intestinal microbiota was significantly lower, while the Shannon index was significantly higher, than those in the rearing water. In the intestine, Chao1 increased initially then stabilized, whereas Shannon declined; in rearing water, Chao1 decreased and then increased, while Shannon showed the opposite trend (P<0.05). PERMANOVA and ANOSIM analyses indicated significant temporal shifts in intestinal communities during growth and persistent differences from rearing-water microbiota (P<0.05). Dominant intestinal phyla were Bacteroidetes, Firmicutes, and Proteobacteria; Bacteroidetes increased significantly after day 46, whereas Firmicutes and Proteobacteria declined. Water microbiota was dominated by Bacteroidetes, Patescibacteria, and Proteobacteria, with the first two phyla increasing and Proteobacteria decreasing over time. At the family level, intestinal communities were enriched in Lachnospiraceae, Muribaculaceae, Prevotellaceae, and Streptococcaceae; the first three families declined significantly after day 46, while Muribaculaceae increased. Water communities were dominated by Clade_I, Flavobacteriaceae, and Rhodobacteraceae, with Clade_I decreasing and the latter two showing a rise-then-fall pattern. Procrustes and source-tracking analyses revealed no significant correlation between intestinal and water communities (P>0.05). Habitat-specificity analysis, random forest modeling, and Mantel tests identified key taxa associated with juvenile growth, and two potentially autochthonous probiotic strains were successfully isolated from the intestine. These findings characterize the temporal dynamics and functional taxa of the intestinal microbiota in juvenile N. albiflora and their relationship to rearing-water communities, providing a foundation for developing host-specific probiotics in this species.