Pomelo peels are rich sources of pectin. The molecular structure and rheological properties of pectin extracted from the endocarp and peel of pomelo fruit were investigated using high-performance liquid chromatography (HPLC), Fourier transform infrared spectroscopy (FT-IR), and rheological analysis. The aim was to facilitate the targeted application of pectins derived from different pomelo tissues and promote the resource utilization of pomelo processing byproducts. The results showed that the galacturonic acid (GalA) contents of endocarp and peel pectins were 75.13% and 87.33%, respectively, while the degrees of esterification were 65.69% and 64.04%, respectively. Both endocarp and peel pectins were classified as high-methoxyl pectins. Endocarp pectin exhibited a significantly higher peak molecular weight (2.02×105 Da) than peel pectin and commercial citrus pectin. The monosaccharide composition of both endocarp and peel pectins was mainly comprised of GalA, rhamnose, arabinose, and galactose. The flow behavior indices of endocarp and peel pectins were 0.508 and 0.635, respectively, both of which were lower than one, indicating pseudoplastic, shear-thinning behavior. Endocarp pectin showed higher apparent viscosity, storage modulus, and loss modulus than peel pectin and commercial citrus pectin, suggesting superior thickening and gelling properties. Overall, a theoretical basis for understanding the structural properties of pectins from different parts of pomelo fruit is provided, and our results support their further exploitation and utilization.