Abstract: Root rot is an important factor that has threatened the cultivation of Panax notoginseng, with an incidence rate of 5% to 20%. Bacterial root rot caused by Pseudomon adaceaecan might only be discovered after infected leaves have wilted, and by then there will no longer be any effective control measures. The objective of this study was to explore the differences in effects of bacterial root rot on the photosynthetic physiological characteristics between control (CK) and diseased plants (DP), thus providing a theoretical basis for the understanding of disease physiology in P. notoginseng. The results showed that the taproot of DP was browned and rotted from root rot, accompanied by broken fibrous roots, decay and hollow stems, withering leaves, and low water content. There was no significant difference in plant height, leaf area, and thickness of leaf antomical strucutres (including thickness of upper epidermis, lower epidermis, palisade tissue, and sponge tissue) between DP and CK. However, the chlorophyll content, net photosynthetic rate (P_n), stomatal conductance (G_s), instantaneous water use efficiency (WUE_inst), intrinsic water use efficiency (WUE_i), and apparent mesophyll conductance (AMC) were significantly lower in DP than in CK (P ≤ 0.05), with intercellular CO₂ concentration (C_i) inversely proportional to P_n in DP individuals. The maximum fluorescence signal of the P700 reaction center (P_m) in DP was not affected during the period of initial infection, but the maximum quantum efficiency of photosystem Ⅱ (PSⅡ) under dark adaptation (F_v/F_m), electron transfer rate of PSⅡETR(Ⅱ), actual photochemical quantum yields of PSⅡY(Ⅱ), electron transfer rate of PSⅠETR(Ⅰ), cyclic electron flow around PSI (CEF), and actual photochemical quantum yields of PSⅠY(Ⅰ) were significantly lower in DP than in CK (P ≤ 0.05). Additionally, the fraction of energy passively dissipated in the forms of heat and fluorescenceY(NO) were significantly higher in DP than in CK (P ≤ 0.05). Furthermore, The K phase in the fast chlorophyll fluorescence kinetic curves was significantly higher in DP than in CK (P ≤ 0.05). Overall, the degree of damage for the various organs of DP was:root>stem>leaf. Root rot significantly degraded leaf chlorophyll, along with irreversible damage to PSⅡ and inhibition of PSⅠelectron transfer and reduced the assimilation ability of mesophyll cells, consequently restricting photosynthetic performance.