To investigate the optimal stocking density for triploid rainbow trout seedlings in high-altitude environments, this study examined three different stocking densities: Low-Density group (LD) with 100 fish per barrel, Medium-Density group (MD) with 200 fish per barrel, and High-Density group (HD) with 300 fish per barrel, over a 60-day cultivation period. The results revealed that the final body weight (Wt) and specific growth rate (SGR) of the LD group were significantly higher than those of the HD group ( P < 0.05). Additionally, the survival rate of the LD group was significantly greater than that of the HD group ( P < 0.05). Variations were observed in the Alpha diversity of both water and gut microbiota at different stocking densities. PCA analysis indicated significant differences ( P < 0.05) in both the water and gut microbiomes among the different aquaculture densities. The dominant phyla in both aquatic and intestinal microbiomes were Proteobacteria, Firmicutes, and Bacteroidetes. Notably, the proportion of Pseudomonas genera was significantly higher in the HD and MD groups compared to the LD group. Co-occurrence network analysis revealed a higher average degree in the LD and MD groups across all densities, suggesting that the microbiota environments of both the intestinal and aquatic ecosystems in these groups were more stable. In conclusion, low-density aquaculture is more suitable for plateau environments. These findings provide valuable insights for the ecological, efficient, and healthy aquaculture of triploid rainbow trout in high-altitude regions.