Intercropping is a key methodology used by farmers to improve economic benefits. However, in certain areas such as Xinjiang, China, limitations in available irrigation water make intercropping difficult to implement. Farmers are therefore challenged to improve economic benefits in water‐limited conditions. We evaluated the effectiveness of intercropped common jujube (Zizyphus jujuba Mill.) and cotton (Gossypium hirsutum L.) under different irrigation regimes. Using a factorial design, crops were planted individually and together (i.e., intercropping) under five different irrigation systems. We measured growth parameters and evaluated the temporal distribution of root system growth and fruit yield. Intercropped cotton displayed higher fitness metrics and outperformed the single‐cropped cotton in crop yield. Intercropping, however, had the opposite effect on jujube plants: the overall fitness and yield of jujube were significantly curtailed under the interspecific competition induced by this planting technique. Under low irrigation levels, cotton plants tended to invade the jujube niches that reduced jujube growth and development. Our findings suggest that in a jujube/cotton intercropping system, cotton is the dominant competitor, whose ability to inhibit the development of the less competitive jujube is exacerbated under water deficit situations. Although intercropping system affected jujube development, overall cotton yield, and therefore benefit to farmers was considerably higher using this system. However, the competitive ability of jujube gradually increases as the plant aged which could reduce the economic advantages of the intercropping system.