Ratoon stunting disease (RSD) of sugarcane is caused by Leifsonia xyli subsp. xyli (Lxx), a kind of gram-positive bacterium. The present study was conducted to observe the pathogenic morphology of RSD and the ultrastructure of RSD-infected stalk, and investigate its effect on photosynthesis of sugarcane under the pathogen stress. Transmission electron microscope (TEM) and scanning electron microscope (SEM) were used to observe the pathogenic morphology and ultrastructure of RSD-infected stalk. Net photosynthetic rate (Pn), stomatal conductance (Gs), intercellular CO2 (Ci) and transpiration rate (Tr) of RSD-infected sugarcane were determined by portable photosynthesis system. The results showed that the modified MSC medium was efficient for Lxx culture. The cell bodies showed various shapes and some had septum and mesosome. They showed uneven cytoplasm with electron transparency, electron dense and septum in the cell bodies. The pathogen and many small granular substances were observed in pits and on surface of the secondary wall of the xylem vessel in RSD-infected sugarcane stalk. The Pn,Gs,Ci and Tr were lower in RSD-infected sugarcane plants than the healthy ones.