Pomelo peel, a by-product of fruit processing, is an excellent source of pectin. We aimed to study the effects of thermal treatments on the extraction and in vitro fermentation patterns of pectins from pomelo peel. We used subcritical water extraction and hot water extraction, with or without chelator (citric acid or EDTA-2Na) assistance to obtain the pectins. The pectin fractions were characterized by their constituent monosaccharide composition and molecular weight (Mw) distribution. The degree of methyl esterification of pomelo pectins was determined using FT-IR spectroscopy. We also compared the fermentation patterns of the pectin using an in vitro simulated human gut fermentation model, monitored Mw changes during fermentation by high performance size exclusion chromatography (HPSEC), and analyzed short-chain fatty acid (SCFA) using gas chromatograph. Our results showed that both chelator assistance and subcritical water treatment increased the pectin yield. Chelator-assisted extraction increased the pectin Mw and decreased the degree of methyl esterification (DM) whereas, subcritical water treatment had the opposite effect. Pectin with low rhamnogalacturonan-I (RG-I) and high homogalacturonan (HG) domain can be obtained from the used pomelo peels by citric acid-assisted extraction. Although gut microbiota intensively utilized uronic acid (UA) of pomelo during early fermentation stages, constituent neutral monosaccharides were consumed even faster than UA. Pomelo pectins enhanced the relative abundance of Bacteroides and Prevotella 9, and stimulated the production of SCFA, particularly acetic acid. Generally, pomelo pectin could be considered a new source for modulating gut microbiota towards a healthy pattern in functional foods.