Jujube–cotton intercropping system is a common efficient practice in China, especially in Xinjiang, Northwest China. While setting up two jujube–cotton intercropping systems, we planted two or four rows of cotton between two rows of jujube to study the formation of yield and factors influencing yield of 1-year jujube on intercropping cotton. The results indicated that photosynthetic/physiological characteristics of cotton in different planting patterns were significantly different only from the squaring stage to prophase of the boll opening stage, and the soil plant analyzer development value were not different all the time. Under the influence of jujube shading, the net photosynthetic rate, stomatal conductance, transpiration rate, and yield of cotton in a four-row cotton intercropping pattern (Int-4) and a two-row cotton intercropping pattern (Int-2) were significantly decreased compared with those of one-row cotton (Sole) and the intercellular CO₂ concentration increased. There was no significant difference between Int-2 and Int-4 in above photosynthetic/physiological characteristics. The higher planting density makes the harvested number and boll number of Int-4 superior. Compared to the Int-2, the yield of Int-4 increased significantly by 10.50%, and the economic benefits from high to low were Int-4 > Int-2 > Sole. Therefore, we concluded that an appropriate increase of cotton planting density is beneficial to the high yield of cotton in a jujube–cotton intercropping system, because it is conducive to increasing the income of farmers.