As primary coffee by-products, Arabica coffee husks are largely discarded during coffee-drying, posing a serious environmental threat. However, coffee husks could be used as potential material for extracting pectin polysaccharides, with high bioactivities and excellent processing properties. Thus, the present study aimed to extract the pectin polysaccharide from Arabica coffee husk(s) (CHP). The CHP yield was calculated after vacuum freeze-drying, and its average molecular weight (Mw) was detected by gel permeation chromatography (GPC). The structural characteristics of CHP were determined by Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), proton nuclear magnetic resonance (1H NMR), and scanning electron microscopy (SEM). Additionally, the rheological and antioxidant properties of CHP and the inhibition capacities of advanced glycation end products (AGEs) with different concentrations were evaluated. The interaction mechanisms between galacturonic acid (GalA) and the AGE receptor were analyzed using molecular docking. The results demonstrated that the CHP yield was 19.13 ± 0.85%, and its Mw was 1.04 × 106 Da. The results of the structural characteristics results revealed that CHP was an amorphous and low-methoxyl pectic polysaccharide linked with an α-(1→6) glycosidic bond, and mainly composed of rhamnose (Rha, 2.55%), galacturonic acid (GalA, 45.01%), ß-N-acetyl glucosamine (GlcNAc, 5.17%), glucose (Glc, 32.29%), galactose (Gal, 6.80%), xylose (Xyl, 0.76%), and arabinose (Ara, 7.42%). The surface microstructure of CHP was rough with cracks, and its aqueous belonged to non-Newtonian fluid with a higher elastic modulus (G'). Furthermore, the results of the antioxidant properties indicated that CHP possessed vigorous antioxidant activities in a dose manner, and the inhibition capacities of AGEs reached their highest of 66.0 ± 0.35% at 1.5 mg/mL of CHP. The molecular docking prediction demonstrated that GalA had a good affinity toward AGE receptors by -6.20 kcal/mol of binding energy. Overall, the study results provide a theoretical basis for broadening the application of CHP in the food industry.