Temperature is a critical environmental factor in fish farming, and the gastrointestinal microbiota plays an important physiological role in host's environmental adaptation. To investigate the structural characteristics of the gastrointestinal microbiota in pond-cultured spotted sea bass (Lateolabrax maculatus) juvenile during the high-temperature period, we conducted a 42-day aquaculture experiment. We analyzed the composition and distribution of the gastrointestinal microbiota using the 16S rRNA high-throughput sequencing method. Results reveal that Aeromonas, Pseudomonas, Enhydrobacter, Acinetobacter, Escherichia-Shigella, Lactobacillus, and Bifidobacterium were the core microbiota in the juvenile gastrointestinal tract after high-temperature acclimation. The microbiota in pond water significantly influenced the structure of the gastrointestinal microbiota. At the end of the experiment, Cetobacterium replaced Acinetobacter as the genus with the highest relative abundance and exhibited antagonistic interactions with Pseudomonas, Acinetobacter, and Enhydrobacter. Additionally, we observed a synergistic relationship between Aeromonas and Bifidobacterium. For the gene enrichment analysis of the gastrointestinal microbiota, we found that the relative abundances of genes involved in pathways such as purine metabolism, pyrimidine metabolism, peptidoglycan biosynthesis, and ribosome pathways increased significantly. This indicates that the microbiota responds to structural dynamics by enhancing their growth and reproductive performance, thereby helping the host adapt to long-term high-temperature environmental acclimation.