Starch-based foods have a large consumer base worldwide. It is known that the quality of freeze-dried starch-based products is subject to deterioration during the production process. The present study was unprecedented carried out to examine the effects of freeze-drying on the cross-linking between components of gelatinized starch-based system. The results showed that the retrogradation of starch in the process of dehydration, the weakening of the binding capacity between the substrate and water of the freeze-dried product and the weakening of the interaction strength between the components of the product were the key mechanisms leading to the quality deterioration of the wheat starch-based conditioned food during the freeze-drying. The addition of lipid and protein can inhibit starch retrogradation during freeze-drying, and the inhibition effect of oil is better. However, the intervention of oil and fat will cause dehydrated starch to re-adsorb the melted oil/water mixture during the freeze-drying process, resulting in the deterioration of product quality. The intervention of protein will improve the binding ability of freeze-dried wheat starch-based product matrix to water. In the ternary system, the intervention of protein will weaken the inhibition effect of lipid on retrogradation of starch in the freeze-drying process. In addition, the lower drying temperature will lead to the decrease of the interaction strength between the components of ternary mixed system. Avoiding the melting of frozen materials during drying is the key control point to improve the quality of freeze-dried wheat starch-based products.