Abstract: Enteromorpha prolifera is a common large-scale alga, which can make filaments grow vertically in the pond in a short time (1—2 weeks). It is a common enemy organism in filter feeding shellfish culture ponds. Once it breaks out, it will not only affect the growth of cultured varieties, but also cause biological diseases and even endanger the survival of cultured varieties, resulting in economic losses. This paper attempts to make use of the habit of Siganus guttatus feeding on Enteromorpha prolifera, and compare Enteromorpha prolifera as a natural bait with artificial feed. In order to study the structure of digestive tract flora, digestive enzyme and nonspecific immune enzyme activity of juvenile Siganus guttatus were fed with artificial feed and Enteromorpha prolifera respectively. High-throughput sequencing technology combined with biochemical analysis methods were used to systematically analyze and compare the composition and distribution of microflora in the stomach, pyloric caecum and intestine of juvenile Siganus guttatus, and to compare the influence on growth performance and digestive enzyme activity of the juvenile Siganus guttatus with the two diets. Biochemical analysis showed that although the growth performance of juvenile Siganus guttatus fed with Enteromorpha prolifera was lower than that of the artificial feed group, its amylase activity was higher than that of the artificial feed group. The juvenile Siganus guttatus had good feeding and digestive ability to Enteromorpha prolifera, which was enough to meet the growth needs of Siganus guttatus. The activities of alkaline phosphatase and superoxide dismutase in the digestive tract of Enteromorpha prolifera group were significantly higher than those in the artificial diet group, showing higher immune and antioxidant capacity. High throughput sequencing results showed that bacterial diversity shows an upward trend with the extension of the digestive tract. The dominant bacteria in the digestive tract were Proteobacteria, Firmicutes and Bacteroidetes. The composition of bacteria in the digestive tract of Siganus guttatus was greatly affected by the diet. The results can provide data support for the bait research of Siganus guttatus. At the same time, it shows that the feeding of Siganus guttatus on Enteromorpha prolifera has a good feasibility basis and significant ecological value, which is worthy of in-depth research and promotion.