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Constipation is a disorder that affects people of all ages. Previous study showed Bifidobacterium spp. altered the faecal concentrations of short-chain fatty acids (SCFAs) while relieving constipation. Therefore, we speculated SCFAs might relieve constipation. We evaluated constipation-related indicators, SCFA levels and the faecal microbiota of constipated mice that were fed acylated starches derived from specific SCFAs for 1 month. It confirmed application of acylated starches resolved the issue of SCFAs absorption in small intestine by measuring the concentration of different SCFA in various tissues. Acetylated starch relieved constipation by increasing acetic acid-producing bacteria that were correlated positively with the small intestinal transit rate and water content of faeces, while butylated starch relieved constipation by increasing butyric acid-producing bacteria that were correlated negatively with the time to the first black stool defecation. These results indicated acetic acid and butyric acid play different roles in relieving constipation.