Prebiotic fermentation by gut microbiota is a key foundation for prebiotics exhibiting physiological functions. However, the relationship among prebiotic type, gut microbiota and gut microbiota metabolism remains unclear. In this study, the gut microbiota of shrimp (Litopenaeus vannamei) was inoculated into medium containing 1% fructooligosaccharide (FOS), galactooligosaccharide (GOS), mannanoligosaccharide (MOS), inulin, β-glucan, isomaltooligosaccharide (IMO) and xylooligosaccharide (XOS). The pH value, digestive enzyme activity, short-chain fatty acid yield and gut microbiota in the fermentation liquid were evaluated. The results showed that after 12 h of in vitro fermentation, β-glucan exhibited the lowest pH value and highest amylase activity among the other types of prebiotics. β-glucan had a higher ability to produce short-chain fatty acids (SCFA) and inhibit the formation of branched-chain fatty acids (BCFA) than the other types of prebiotics. At the genus level, β-glucan markedly promoted the growth of Bacillus. These findings suggest that β-glucan was the most suitable type of prebiotic and had greater prebiotic effects than the other types of prebiotics on the basis of in vitro fermentation by the gut microbiota of shrimp (Litopenaeus vannamei).