An in vitro gastrointestinal model consisting of oral, gastric, and intestinal phases was used to elucidate the impact of pectin on the digestion of emulsified lipids. Pectin reduced the extent of lipid digestion, which was attributed to its binding interactions with specific gastrointestinal components. The interaction of pectin with bile salts, lipase, CaCl2, and NaCl was therefore investigated by turbidity, microstructure, electrophoresis, and isothermal titration calorimetry (ITC) at pH 7.0 and 37 °C. ITC showed that the interaction of pectin was endothermic with bile salts, but exothermic with CaCl2, NaCl, and lipase. Electrophoresis, microstructure, and turbidity measurements showed that anionic pectin formed electrostatic complexes with calcium ions, which may have decreased lipid digestion due to increased lipid flocculation or microgel formation because this would reduce the surface area of lipid exposed to the lipase. This research provides valuable insights into the physicochemical and molecular mechanisms of the interaction of pectin with gastrointestinal components that may affect the rate and extent of lipid digestion.