The yield and quality of Medicago sativa are seriously affected by the fungal pathogen Phoma medicaginis. A study has been undertaken using growth chamber pot experiments and the LI-6400/XT photosynthesis measurement system to investigate the effects of this pathogen on the photosynthetic physiology of M. sativa. The results showed that until 27 days post-inoculation (dpi) the net photosynthetic rate (Pn), stomatal conductance (Gs) and transpiration rate (Tr) of M. sativa were reduced by P. medicaginis infection. In the early stages of infection there were little changes in intercellular CO2 concentration (Ci) in the leaves. By 23 dpi, infected leaves showed significant reductions in photochemical quantum efficiency (Fv/Fm), PSⅡ reaction center of excitation energy capture efficiency (Fv'/Fm'), the relative quantum efficiency of PSⅡ photochemistry (ΦPSⅡ), electron transfer rate (ETR), photochemical quenching (qP) and non-photochemical quenching (qN). Light compensation point, CO2 compensation point and carboxylation efficiency (CE) also decreased. The results indicate that the photosynthetic electron transfer rate and capture efficiency, non-photochemical quenching (qN), and carboxylation efficiency (CE) decreased in leaves infected by P. medicaginis, leading to light suppression and a decrease in the assimilation of CO2 that affect the growth and development of M. sativa.