Dietary carbohydrates are anaerobically fermented by gut microbiota to short-chain fatty acids (SCFAs), conferring gut health benefits. Of all tested prebiotics, galactooligosaccharides (GOS) and resistant starch (RS) stimulated the SCFA production in mud crab (), a crustacean model, to a greater extent than the other carbohydrates tested. Using anaerobic fermentation cultures, this study further explored the prebiotic potential of GOS and RS in mud crab by assessing their impacts on gut microbiota changes and SCFA production. Both GOS and RS significantly promoted SCFA production. Bacterial diversity in the GOS group was lower than in the RS or control group. GOS promoted the growth of Bacteroidetes, while RS promoted Tenericutes. A strong positive correlation was found between SCFA production and bacterial abundance; most bacteria correlated with each other. The findings demonstrated the prebiotic potential of GOS and RS in mud crab.