The change in temperature will change the composition of intestinal microorganisms of juvenile Eriocheir sinensis, and the composition of intestinal microorganisms will affect the growth and development of juvenile crabs. In order to explore the relationship between intestinal microorganisms and growth of E. sinensis at different temperatures, the status of growth and intestinal microflora of juvenile E. sinensis reared at different water temperatures (15 °C, 23 °C, and 30 °C) were compared in this study. The results showed that the respective survival rate of juvenile E. sinensis in the three water temperature groups was 100%, 87.5%, and 64.44%. Moreover, the molting rate increased with an increase in water temperature, which was at 0%, 10%, and 71.11% for the three respective temperature groups. The average weight gain rate showed an overall increasing trend with the increase of water temperature. Moreover, the final fatness of the crabs in the 30 °C water temperature group was significantly lower than that in the 15 °C and 23 °C groups (p < 0.05); there was no significant difference in the liver-to-body ratio among the three groups. The results of the alpha diversity analysis of the 16S rRNA data revealed that there was no significant difference in the intestinal microbial abundance among the three water temperature groups; however, the intestinal microbial diversity in the 23 °C water temperature group was significantly lower than that in the 15 °C and 30 °C groups. At the phylum level, the dominant flora of the three groups was Firmicutes, Proteobacteria, and Bacteroidota. At the genus level, the abundance of Parabacteroides and Aeromonas in the intestine of the crabs in the 30 °C water temperature group was significantly higher than that in the 15 °C and 23 °C groups (p < 0.05). The function prediction showed that the main functional diversity of intestinal microflora of juvenile E. sinensis in the three water temperature groups was similar and mainly involved in metabolic-related functions, but there were still differences in the effects of water temperature on functional pathways such as metabolism, immunity, and growth among each group, either promoting or inhibiting. In conclusion, different water temperatures can affect the composition and function of intestinal flora of E. sinensis, and 23 °C–30 °C is the optimal water temperature for the growth of juvenile E. sinensis.