Lobophytum is a valuable component of the coral reef ecosystem and is commonly traded in the marine aquarium industry. Its natural metabolites exhibit promising physiological activities, including anti-inflammatory, anti-viral, and anti-infectious properties, indicating significant medicinal potential. Zooxanthellae, brown unicellular algae, engage in a mutually beneficial relationship with corals, providing essential energy through photosynthesis for the growth and metabolism of the coral symbionts. The health and abundance of zooxanthellae play a crucial role in the physiological cycle of coral symbionts. The prokaryotic composition within coral symbionts is highly diverse, with dominant microorganisms including α-proteobacteria, γ-proteobacteria, β-proteobacteria, and Bacteriodetes. This microbial composition significantly impacts coral health. In recent years, the increasing severity of coral reef bleaching due to environmental changes has prompted a focus on reef-building corals, while research on soft corals has primarily centered on their bioactive compounds, with less attention on other aspects. The gradual eutrophication of near-shore waters has led to a rise in coral stress factors. Understanding the composition of zooxanthellae and symbiotic bacterial communities is crucial for assessing coral health and comprehending coral's environmental adaptations, enabling the development of effective conservation strategies. In this study, we cultured Lobophytum sp. in different water qualities for one month and analyzed the community structure of zooxanthellae, ambient water bacteria, and symbiotic bacteria using high-throughput sequencing technology. The water quality parameters were consistent across the three experimental groups, with differences in nitrate nitrogen and phosphate levels. Group 1 had nitrate nitrogen <10 mg/L, phosphate <0.2 mg/L, group 2 had nitrate nitrogen <50 mg/L, phosphate <0.5 mg/L, and group 3 had nitrate nitrogen <5 mg/L, phosphate <0.1 mg/L. The findings indicated that all corals survived, and there were no significant differences in tentacle extension vitality between the groups, leading to the conclusion that the set water quality indicators met the conditions for coral survival. Cladocopium sp. dominated the zooxanthellae for all three coral groups, with a relative abundance ranging from 70.25% to 98.13%, suggesting a low tolerance for high nutrient salts and a significant decrease in abundance. In contrast, Symbiodinium sp. showed less sensitivity to water nutrients, with a relative abundance ranging from 0.75% to 1.14%. The densities of zooxanthellae were notably reduced when ambient nitrate nitrogen was < 5 mg/L and phosphate was < 0.1 mg/L, as evidenced by a decrease in the Chao index from 21.00 to 14.00 and a decrease in the Ace index from 22.82 to 14.00. At the phylum level, environmental and coral symbiotic bacteria differed in abundance, with all dominant bacterial populations belonging to Proteobacteria, ranging from 45.63% to 86.55% in relative abundance. Additionally, the environmental bacterial diversity at the genus level (Shannon index 4.60 - 4.97) was higher than that of coral symbiotic bacteria (Shannon index 2.58 - 3.81), and the two dominant bacterial populations were relatively independent. The coral symbiotic bacterium Cohaesibacter exhibited low-nutrient salinity tolerance, with its abundance increasing significantly with decreasing nutrient salinity, from < 3% to 40.27%. This genus of soft corals demonstrated high adaptability to symbiotic bacteria Vibrio, with no significant anomalies observed at 23.71% abundance of Vibrio. The Venn diagram showed that the three groups of corals shared the same 8 species of zooxanthellae, and the three groups of environmental waters and corals shared 85 species of bacteria. These results suggest that the abundance of zooxanthellae and symbiotic bacteria can be influenced by ambient water, leading to changes in the dominant bacteria and community structure of symbiotic bacteria for coral. Moreover, the diversity of symbiotic bacteria showed significant differences, and compared to the environmental bacterial community, fluctuations in environmental nutrient salts had a greater impact on the population structure of symbiotic coral bacteria. This experiment contributes to enriching the research field of soft corals, providing a theoretical basis for understanding the dynamic effects of different water quality indicators on the structure of symbiotic microorganisms in soft corals. Additionally, it helps to study the impact of water quality fluctuations on soft coral zooxanthellae and bacterial community structure in artificial environments, and assists in the development of coral conservation programs.