This study investigated correlations between gut microbiota and type 2 diabetic (T2D) indexes using either native resistant starch (RS, from high amylose maize starch, HAMS) or acylated starch via short-chain fatty acids (SCFAs) acylation. Compared to HAMS, consumption of acylated starch achieved a greater impact on the improvement of T2D indexes in term of body weight loss, fasting blood glucose, serum insulin level and amino acid metabolism. Intervention with acylated starches alleviated metabolism disorders and modified the gut microbiota. This study found all the acylated starch significantly enhanced the growth of SCFAs-producing bacteria compared to its native HAMS, and this change was highly consistent with their corresponding SCFAs concentration both in serum and fecal samples. This is the first reported to reveal that propionylated HAMS promoted the abundance of Bifidobacterium, while acetylated and butylated HAMS benefited the enrichment of Coprococcus, Butyricimonas and Blautia, which may indicate their different intervention pathway.