The physicochemical properties, biological functions and microbial degradation of inulins differ according to their degree of polymerization. However, the relationship between inulin activities and its effect on gut microbiota remains unknown. In this study, high fat diet with inulin (1 or 5 g/kg·bw), either with short or long chains groups were administered to different groups of mice (n = 10) for 10 weeks in order to investigate the effect of inulin on the microbial diversity of the animals. Litchi pericarp procyanidins (LPPC) were used for comparison purposes. Furthermore, the lipid metabolism and key regulator genes in mice were determined. The results indicated that natural inulin (1 g/kg·bw) ingestion reduced the body weight of fat mice between week 6-9. Glutathione peroxidase (GSH-Px) activity in liver was remarkably higher after adding long chain inulin (5 g/kg·bw) compared to high-fat-diet mice. Moreover, high dose of natural inulin regulated malondialdehyde and advanced glycation end-products levels in mice liver. Likewise, the high dose of short-chain inulin increased sterol response element binding protein 1 (SREBP-1), β-Hydroxy β-methylglutaryl-CoA (HMG-CoA) and ATP-binding cassette transporter A1 (ABCA1) genetic expression. A significant change on the abundance of six genera in gut microbial profile suggested that inulin has the ability to modulate the lipid metabolism regardless of chain length, mainly due to its impact on colon microbiota variety.