The yellowtail kingfish (Seriola lalandi) is a globally distributed marine economic fish. The consumer demand for this fish is growing because of its delicious taste and high nutritional value. With increasing catch numbers, its natural resources are gradually declining. Many countries, including China, have begun to artificially culture this species. We found that the development of the juvenile yellowtail kingfish gastrointestinal tract (stomach, pyloric caecum, and gut) was evident and strong, with a fast growth rate. Evaluating the characteristics of microbiota structure may contribute to analyzing the effect of the microbiota, introduced by feed, on the change rule of gastrointestinal tract microbiota during nutrient metabolism. In this study, 16S rDNA high-throughput sequencing was used to assess the characteristics of gastrointestinal tract microbiota structure of yellowtail kingfish juveniles during the whole feeding cycle and analyze the correlation with the microbiota in feed. Results showed that Lactobacillus, Pseudomonas, Acinetobacter, Sphingomonas, Bacteroides, Aeromonas, Vibrio, and Faecalibacterium were the shared and dominant genera colonizing the stomach, pyloric caecum, and gut. In combination with the changes in dominant genera during nutrient metabolism, Lactobacillus, Enterovibrio, Bifidobacterium, Pseudomonas, Acinetobacter, Bacillus, Escherichia-Shigella, Paenibacillus, Sphingomonas, Bacteroides, Methylomonas, Streptomyces, Aeromonas, Vibrio and Faecalibacterium were selected as the core microbiota in the gastrointestinal tract of yellowtail kingfish juveniles. These core microbiota contained both potential probiotics and pathogens; the relationship between the potential probiotics and pathogens in the gastrointestinal tract was maintained in a dynamic balance during nutrient metabolism of the host, which will protect the health of the host from a microecological perspective. Through analysis of the evolution trend of dominant microbiota structure, it was found that the microbiota introduced by feed had a great influence on the relative abundances of gastrointestinal tract microbiota during nutrient metabolism, which revealed the importance of the safety of the microbiota in feed. Our findings provide theoretical support for the screening of local probiotics of yellowtail kingfish juveniles and a reference for healthy culture management of the species.