The study aimed to find the best Arbuscular Mycorrhizal Fungi (AMF) strain for cotton growth in Xinjiang's salinity and alkali conditions. Cotton (Xinluzao 45) was treated with Funneliformis mosseae (GM), Rhizophagus irregularis (GI), and Claroideoglomus etunicatum (GE) as treatments, while untreated cotton served as the control (CK). Salinity stress was applied post-3-leaf stage in cotton. The study analyzed cotton's reactions to diverse saline-alkali stresses, focusing on nutrient processes and metabolism. By analyzing the growth and photosynthetic characteristics of plants inoculated with Funneliformis mosseae to evaluate its salt tolerance. Saline-alkali stress reduced chlorophyll and hindered photosynthesis, hampering cotton growth. However, AMF inoculation mitigated these effects, enhancing photosynthetic rates, CO2 concentration, transpiration, energy use efficiency, and overall cotton growth under similar stress levels. GM and GE treatments yielded similar positive effects. AMF inoculation enhanced cotton plant height and biomass. In GM treatment, cotton exhibited notably higher root length than other treatments, showing superior growth under various conditions. In summary, GM-treated cotton had the highest infection rate, followed by GE-treated cotton, with GI-treated cotton having the lowest rate (GM averaging 0.95). Cotton inoculated with Funneliformis mosseae, Rhizophagus irregularis, and Claroideoglomus etunicatum juvenile showed enhanced chlorophyll and photosynthetic levels, reducing salinity effects. Funneliformis mosseae had the most significant positive impact.