Pectin is an acidic heteropolysaccharide with natural, green, and inexpensive characteristics. Compared to polysaccharides, oligosaccharides are more easily utilized by the body, and the physiological function of hawthorn pectin oligosaccharides (POS) may vary depending on their degree of polymerization (DP). Therefore, we mainly studied the effects of hawthorn pectin (HP) and POS with different DP on gut microbiota disorders induced by high-fat diet (HFD). HP and POS both improved weight gain, dyslipidemia, and glucose homeostasis caused by HFD, and increased serum GLP-1 levels. Meanwhile, the increased expression of Gcg and Pcsk1 genes in the ileum of the treatment group further confirmed this result. In addition, HP and POS reduced certain opportunistic pathogens, while restoring the richness and diversity of the gut microbiota. Meanwhile, HP and POS can improve intestinal barrier dysfunction by increasing the claudin-1, occludin, ZO-1, and MUC2 genes. Furthermore, fecal metabolomics suggests that POS may enhance linoleic acid synthesis and improve lipid metabolism by upregulating 9,10-DHOME ((12