The differences in composition and activity of pectin polysaccharides in the cell walls of Goji berry peel and flesh were investigated using the cell wall pectin polysaccharides extracted from them. The basic structural characteristics of the cell wall pectin polysaccharides were analyzed using ultraviolet–visible spectrophotometry and Fourier–transform infrared spectroscopy. Monosaccharide composition and molecular weight distribution of the cell wall pectin polysaccharides were determined using anion exchange chromatography and gel permeation chromatography. The inhibitory effects on pancreatic lipase and α-amylase were measured via enzymatic activity inhibition experiments. The results indicated that the cell wall pectin polysaccharide content in Goji berry peel was significantly higher than that in the flesh (P<0.05). Cell wall pectin polysaccharides of both the peel and flesh were primarily composed of arabinose, galactose, galacturonic acid, rhamnose, xylose, and glucose, with peel pectin polysaccharides having a higher molecular weight. The half-maximal inhibitory concentration (IC50) of flesh pectin polysaccharides against pancreatic lipase was 4.334 mg•mL-1, indicating a stronger inhibitory effect than the peel. However, peel pectin polysaccharides demonstrated a superior inhibitory effect on α-amylase (IC50: 6.939 mg•mL-1) to the flesh pectin polysaccharides. Both types of pectin polysaccharides exhibited mixed-type inhibition, suggesting that the peel and flesh pectin polysaccharides can potentially regulate glucose and lipid metabolism. The results of this study provide a theoretical basis and novel approach for the high-value utilization of peel residue by-products derived from Goji berry processing.