Pectin with various degrees of esterification (DE) leads to different food processing directions and has the distinct potential for modulating human health. Investigations of pectin-gut microbiota interactions may contribute towards better understanding of the structure-function mechanism. In this study, in vitro batch fermentation (artificial colon model) was used to illustrate the differential impacts of pectin with different DE on the gut microbiota and metabolome of healthy adults. The results indicated that low-esterified pectin L13 showed better-sustained abilities in terms of the diversity of microbiota and promoted the abundance of Clostridiaceae and Lachnospiraceae at family levels, and Bacteroides and Lachnospira at genus levels. High-esterified pectin H121 induced less Enterococcus and Clostridium. Data from untargeted metabolomics revealed the alterations of intracellular metabolites including fatty acids, amino acids, and organic molecules by various types of pectins. Inositol was the unique intracellular metabolite that was significantly upregulated by low-esterified pectin L13. All types of pectins could increase the level of acetic acid, but butyric acid was only enriched by pectin L13.