The seeds of cotton ‘Dalingmian No.69’ were used as the material in the pot experiment. We inoculated two species of arbuscular mycorrhizal fungi (AMF) including Rhizophagus intraradices (RI) and Funneliformis mosseae (FM) into the cotton roots respectively, in order to investigate the effects of AMF on cotton growth, root characteristics, cell membrane permeability, antioxidant enzyme activities and the accumulation and transfer of arsenic in cotton under different soil arsenic concentrations (0, 100, 200 mg/kg). It provided the theoretical basis for the reasonable application of AMF in the remediation of arsenic contaminated soil. The results showed that: (1) cotton growth, root development, root activity, antioxidant system (SOD, POD, CAT) and osmotic regulation system (soluble sugar, soluble protein, proline) were inhibited with the aggravation of arsenic stress. (2) Inoculating RI or FM significantly increased the plant height, biomass, rootshoot ratio and root activity of cotton. The arsenic content of the aboveground and underground parts and transfer coefficient of cotton were reduced. The root morphological indexes (such as total root length, root surface area, root volume, root tip number and root branch number) were also enhanced by RI or FM inoculation. The root length percentage of 0-0.2 mm diameter class was decreased, but the root length percentage of 0.5-1.0 mm and >1.0 mm diameter class were increased. With RI or FM inoculation increased, the contents of osmotic regulatory substances (such as soluble sugar, soluble protein and proline) and the activities of antioxidant enzymes (such as SOD, POD and CAT) in the cotton leaves and roots at different levels. The relative conductivity and malondialdehyde(MDA) content were decreased by RI or FM inoculation, and the effects of F. mosseae inoculation was greater than that of R. intraradices inoculation. It was concluded that AMF inoculation reduce arsenic toxicity to cotton, and enhance the tolerance of cotton under soil arsenic stress by promoting cotton growth and root development, reducing arsenic concentration in cotton, inhibiting its transfer to the ground, and activating antioxidant system and osmotic regulation system, and the inoculation effects of F. mosseae was better than that of R. intraradices.