Abstract: Intestinal microbiome is regarded as the "second genome" of host. Comprehending the influences of external factors on the structure of the intestinal microbial community in juvenile Chinese sturgeon (Acipenser sinensis) can provide a reference for its healthy breeding. Taking 50 DAH A. sinensis juvenile as objects, we applied the high-throughput sequencing technology to analyze the characteristics of intestine and intestinal content, and explore their correlation with feed and culture source water. The results show that on genus level, there were differences in the microbial composition between intestine and intestinal content. The intestine was mainly composed of Acinetobacter, Lactococcus, Citrobacter, Pseudomonas and Clostridium_sensu_stricto_1, while the intestinal content was mainly composed of Lactococcus, Clostridium_sensu_stricto_1 and Terrisporobacter. Source Tracker analysis verified that 82.68% of the intestine community came from the feed, and 1.89% came from the culture source water. While 94.60% of the intestinal content community came from the feed, and 0.93% came from the culture source water. The study indicates that there are differences in the microbial composition of the intestine and intestinal content of the juvenile on genus level. The dominant bacterial genera in the former are mostly potential pathogenic bacteria, while those in the latter are mostly beneficial bacteria. Compared with the culture source water, the feed has a higher contribution to the composition of the intestine and intestinal content microbial community.