The physiological function of thermally treated starch-based foods was predictively analyzed by in vitro fermentation. Different thermal treatments affected the structure of resistant starch and the presence of harmful substances. The effect of these treatments on their in vitro fermentation properties was emphasized. In this study, undigested components with different structural characteristics were isolated from starch–protein–oil mixtures treated by thermal treatments (boiling, baking, and frying). The structures of digested residues from different thermally treated ternary mixtures were disrupted to varying degrees compared with the control, as evidenced by the reduction of crystalline regions, the break of inter-molecular hydrogen bonds, and damage to molecular structure of rice starch. Baking (1.381 μg/g) and frying (1.696 μg/g) resulted in higher contents of Maillard reaction products (AGEs) than boiling (1.246 μg/g). After fermentation, the content of short-chain fatty acids generated by thermally treated ternary mixtures lowered, correlating with the incomplete structure of resistant starch. By contrast, the species diversity of intestinal microbes increased in thermally treated groups because of their high intestinal pH, which favored the growth of pathogenic bacteria. In addition, the Bacteroidetes/Parabacteroides ratio of the dominant microbes in thermally treated groups was reduced, which was detrimental to the maintenance of intestinal homeostasis. In particular, the high AGE content in baking and frying groups increased the relative abundance of harmful microbes such as Proteobacteria and Pseudomonas.