[Objective] The effect of arbuscular mycorrhizal fungi (AMF) inoculation on photosynthetic characteristics and mesophyll cell ultrastructure in cotton under arsenic stress were studied. [Method] Cotton germplasm Dalingmian 69 were used as the test material in the pot experiment. Two species of AMF including Rhizophagus intraradices and Funneliformis mosseae were inoculated into the cotton roots respectively in order to investigate the effects of AMF on stomatal morphological characteristics, gas exchange parameters, chlorophyll fluorescence parameters and mesophyll cell ultrastructure under different arsenic concentrations (0, 100, 200 mg·kg-1) in soil. [Result] (1) Arsenic stress significantly reduced stomatal length, width, density, conductance, transpiration rate, intercellular CO2 concentration and net photosynthetic rate, and significantly affected chlorophyll fluorescence parameters of cotton leaves. However, compared with the control treatment, inoculation of AMF increased the length, width, aperture, density, and conductance of cotton stomata, and significantly increased the net photosynthetic rate, transpiration rate, intercellular CO2 concentration, actual photosynthetic efficiency, the maximum photochemical quantum yield and photochemical quenching coefficient, and reduced the non-photochemical quenching coefficient under different concentrations of arsenic. Under 100 and 200 mg·kg-1 arsenic concentration, the net photosynthetic rate and actual photosynthetic efficiency of F. mosseae treatment were significantly higher than those of R. intraradices treatment. (2) Arsenic stress led to the gradual swelling of chloroplast, the overall structure was destroyed, the disordered and uneven arrangement of grana thylakoids, the loose and deformed arrangement of cristae in mitochondria, the appearance of voids in some mitochondrial structures, and the fuzzy double-layer membrane structure. However, under arsenic stress, the lamellae of chloroplast grana in the mesophyll cells of cotton inoculated with AMF were clearly visible, and the cristae in mitochondria were closely arranged, and the degree of arsenic damage was significantly reduced. The palliative effect of F. mosseae was even stronger. [Conclusion] Under arsenic stress, inoculation of F. mosseae and R. intraradices significantly increased the net photosynthetic rate and light energy utilization efficiency, and improved the photosynthetic capacity of cotton, and reduced the damage of arsenic to the ultrastructure of mesophyll cells. And the inoculation effect of F. mosseae was better.