The infrared spectroscopy method is employed to analyze the corn leaves infected by the southern corn leaf blight disease and the molecular structure information of infected corn leaves is obtained. The research results show that the fungal pathogens have certain effects on the protein structure of the leaves. The two-dimensional correlation infrared spectral analysis indicates that the β-sheet conformation of the protein secondary structure in healthy corn leaves changes with the growth and metabolism of corn leaves, while in the infected corn leaves is the change of the β-turn conformation. Two-dimensional correlation infrared spectroscopy can be used to reveal the change of molecular structures of corn leaves invaded by the fungal pathogens and provide a reference for the prevention and control of corn diseases.