The linear amylose in starch forms inclusion complexes (ICs) with numerous nonpolar ligand molecules. Starch ICs, a type of supramolecular host–guest assembly, have key roles in the digestion, nutrient intake, and health effects of starch-containing diets. In particular, the development of ICs has been predicted to reduce the rate and extent of enzymatic digestion of starchy foods. The binding forces of host–guest components are generally weak bonds like electrostatic interactions, van der Waals force, and hydrogen bonds. Literature surveys reveal that the V-type starch acts as a reliable delivery system to encapsulate lipids, aroma compounds, fatty acids, phytochemicals, and so on. The incorporation of starch ICs into food products has led to improvements in both functional and nutritional value. This review summarizes the recent advancements and shortcomings in the starch inclusion complex. The article is divided into three parts explaining the (1) benefits of resistant starch and IC formation mechanism and (2) encapsulation of bioactive compounds, including fatty acids, phenolic, and aromatic compounds. (3) Modification techniques to enhance resistant starch content and improve digestibility. Food processing and modifications are complex and involve several non-linear relationships that can be difficult to model. The application of artificial neural networks in processes such as extrusion, encapsulation, and shelf-life estimation reduces the need for repeated experiments and aids in identifying optimal parameters.