Photosynthesis is the basis of crop growth and is sensitive to stress. Smut (Sporisorium destruens) is the primary disease in the production of broomcorn millet (Panicum miliaceum L.). This study evaluated the effects of infection with S. destruens on the photosynthesis of the resistant cultivar (BM) and susceptible cultivar (NF). After inoculation, there was a decrease in the chlorophyll content, gas exchange parameters, and chlorophyll fluorescence of the two cultivars. Observation of the ultrastructure of diseased leaves showed that the chloroplasts and mitochondria had abnormal morphology, and some vacuoles appeared. RNA-seq was performed on the flag leaves after inoculation. In addition to the resistant and susceptible cultivars, the diseased leaves developed from inflorescences were defined as S2. The analysis showed that the pathways related to photosynthesis stimulated some differentially expressed genes (DEGs) after infection with S. destruens. More DEGs were induced in the susceptible broomcorn millet NF than in the resistant broomcorn millet BM, and most of those genes were downregulated. The number of DEGs induced by S2 was greater than that in susceptible cultivar NF, and most of them were upregulated. These results indicate that infection with S. destruens affects the normal photosynthetic performance of broomcorn millet. Understanding the mechanism between S. destruens, photosynthesis, and broomcorn millet is an effective measure to prevent the occurrence of smut and enhance its resistance.