The objective of this study is to clarify the effects of jujube-cotton intercropping on cotton yield and photosynthetic characteristics, to provide a theoretical basis for jujube-cotton intercropping in the oasis irrigation area of southern Xinjiang, and to provide new ideas for local farmers to improve their economic benefits. In this study, the effects of jujube-cotton intercropping on the photosynthetic characteristics and yield of cotton were studied from 2020 to 2023 using Zhongmian 619 cotton and juvenile jujube trees as experimental materials. The changes of lower leaf area index (LAI), transpiration rate (Tr), stomatal conductance (Gs), net photosynthetic rate (Pn), intercellular CO2 concentration (Ci), yield and economic benefits were evaluated in different years. The results showed that: (1) There was a positive correlation between leaf area index (LAI) and photosynthetic characteristics of cotton under different planting patterns; Compared with monoculture cotton, the net photosynthetic rate (Pn), stomatal conductance (Gs) and transpiration rate (Tr) of jujube-cotton intercropping were lower than those of monoculture cotton in the intercropping mode. At the peak boll stage, the photosynthetic characteristics of monoculture cotton were significantly higher than those of intercropping cotton, indicating that the intercropping pattern of jujube cotton affected the photosynthesis of cotton to a certain extent. (2) From 2020 to 2023, the land equivalent ratio (LER) of jujube-cotton intercropping was greater than 1, and the overall yield and economic benefit of jujube-cotton intercropping system were higher than those of cotton monoculture and jujube monoculture, especially in 2023, the yield of IC treatment was as high as 55.35%. (3) From 2020 to 2023, there was a significant positive correlation between cotton yield and leaf area index (LAI). In conclusion, intercropping cotton can improve the land equivalent ratio and land utilization rate by improving the photosynthetic characteristics, and increase the economic benefits and total yield of juvenile jujube orchards.