Processing will improve the digestion of corn by ruminant animals. The objectives of this study were to investigate the effects of processing methods (grinding, G; steam flaking, SF; extrusion, E) on the starch properties, nutrient profiles, in vitro ruminal fermentation and molecular structure of corn. Compared with G, SF and E increased (p < 0.05) the starch content, starch gelatinization, ruminal gas production (GP, 0.5–32 h), propionic acid, starch degradability (SD), the area and height of carbohydrate peaks, and decreased (p < 0.05) starch crystallinity, content of crude protein, neutral detergent fiber and acid detergent fiber, ruminal NH3-N, the area and height of amide I and II, α-helix, and β-sheet. The total VFA (24 h, 48 h) tended to be increased by SF and E (p < 0.10). The carbohydrate peak area and height were positively (p < 0.05) correlated with GP (1–24 h) and SD. The protein molecular absorption intensity was negatively correlated with SD (p < 0.05). The change in starch properties, GP (1–24 h) and molecular structure caused by E was greater than SF (p < 0.05). These results indicated that the higher starch gelatinization and lower starch crystallinity of E corn, induced by the high temperature and pressure, enabled more fermentation and digestion in the artificial rumen. The carbohydrate and protein molecular structures were correlated with the nutritional characteristics of corn.