Background Pectin exists in a broad range of plants, and acts as functional food additives with modulatory effects on colonic inflammation and metabolism dysfunctions, which underscores its promising prospects in commercialization. Moreover, food ingredients like pectin can impact the gut microbiota, and the degradation capabilities of these commensals may in turn determine the efficacy of dietary intervention. Scope and approach In this review, the pectin-host axis was figured by summarizing the physiological functions of pectin and the associated mechanisms; The pectin-gut microbiota axis was described via discussing the impact of pectin on intestinal microbiota composition; And the gut microbiota-host axis was discussed through describing the beneficial functions of pectinolytic commensals and their metabolites. Key findings and conclusions The structure properties of pectin including degree of esterification and branched chains played critical roles in their physiological functions of metabolism regulation, inflammation modulation, and carcinogen prevention. Meanwhile, distinct diversity, enterotypes or composition of gut microbiota can be developed under interventions of pectin with various structure characteristics, and pectin-induced dominant bacteria like Ruminococcaceae, Succinivibrionaceae, Lachnospiraceae and Bacteroidaceae and their metabolites exhibited relevant health-promoting functions. All these data are fundamental to establish the precise networks and further discover underlying mechanisms of pectin-gut microbiota-host interactions and can optimize the development of pectin in food and health care products.