Growth is one of the most important economic traits in aquaculture and is directly related to the financial benefits of farming. It is influenced by a number of factors, including genetic and environmental factors. When faced with different environments, fish growth is not only regulated by their own physiological conditions but also by symbionts, such as gastrointestinal microbiota. To investigate the differences in the growth of yellowtail kingfish juveniles under two culture modes, namely indoor tank and deep sea cage culture, and their relationship with gastrointestinal flora, as well as with feed microbiota and culture water microbiota, six-month-old fish of the same size at (17.23±0.99) cm and body mass at (77.44±11.58) g were selected for a 30-day culture experiment under these two culture modes. The differences in the rate of yellowtail kingfish juvenile growth under these two culture modes were recorded. The structure and abundance of gastrointestinal microbiota (stomach, pyloric blind sac, and intestine), as well as feed and culture water microbiota, were analyzed by 16S rRNA high-throughput sequencing and bioinformatic analysis. The results showed that the growth of cage cultured juvenile yellowtail kingfish was significantly faster than that of indoor tank cultured fish. As for the gastrointestinal microbiota of juveniles cultured in cage, the abundance of Bacteroidetes and Firmicutes at the phylum level, as well as the abundance of Alloprevotella and Bacteroides at the genus level, were higher than in indoor tank cultured fish, wherein the abundance of Bacteroides was significantly higher. The composition of the gastrointestinal microbiota of the indoor tank cultured fish was different from that of the feed microbiota and significantly different from that of culture water microbiota, whereas the composition of the gastrointestinal microbiota of fish from cage culture was more similar with that of the feed microbiota but also significantly different from that of the culture water microbiota. Beta diversity analysis showed that the gastrointestinal microbiota of juvenile yellowtail kingfish was more influenced by feed microbiota and less by the culture water bacterial community. KEGG annotation analysis showed that the main functional pathways involved in the gastrointestinal microbiota of juvenile yellowtail kingfish in the cage culture were the phosphotransferase system (PTS) and NOD-like receptor signaling pathway, whereas carbohydrate metabolism and the carotenoid biosynthesis pathway were found in the indoor tank cultured fish. These results indicate that the gastrointestinal microbiota regulate the growth of yellowtail kingfish juveniles under indoor tank and cage culture conditions by changing their structure and abundance, as well as via functional pathways. Moreover, feed microbiota had a greater influence on gastrointestinal microbiota than culture water microbiota. According to these results, the faster growth of cage cultured fish may be due to the production of more short-chain fatty acid (SCFA) by gastrointestinal microbiota (e.g., Alloprevotella and Bacteroides) to induce the production of insulin-like growth factor 1 (IGF-1). These findings provide micro-ecological support for high-efficient commercial feed and healthy culture technology for yellowtail kingfish.