In this project, a one-month field study was carried out to reveal the food-habitat relation and the adaptation process of a tropical sea cucumber Stichopus chloronotus with specific habitat preference, using in situ mesocosm method with three single habitat type treatments. Microbial community structure change of gut contents revealed by high throughput sequencing analysis based on 16S rRNA was used as the biomarker, exploring the changes in microbial community structure in the gut contents of S. chloronotus under specific habitat types (sandy bottom, broken coral branches bottom and reef bottom), and revealing their selection ability to specific sediments and prokaryotes.