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The photosynthetic characteristics of jujube—cotton intercropping system under different cropping patterns and drip irrigation modes were studied in the southern desert oasis region of Xinjiang. The objective was to analyze the water use of cotton in intercropping system under water-saving conditions. Totally nine treatments were carried out, which were jujube—cotton spacing of 80cm (J—1), 100cm (J—2) and 120cm (J—3), the control monoculture of jujube (CK—Z), control monoculture of cotton (CK—M) and different irrigation quotas of G—1 (45mm), G—2 (60mm), G—3 (75mm) and G—4 (90mm). Results showed that water demand of jujube at shoots growing stage was relatively larger than cotton, photosynthesis and transpiration rate with lower drip irrigation quota (45mm) were significantly lower than those of other four treatments, but at this stage (cotton was at bud stage), the moisture had less effect on photosynthesis and transpiration rate of cotton. In addition, excessive irrigation (90mm) also could reduce cotton photosynthetic. Changes of stomatal conductance were similar with transpiration rate, these parameters of jujube for G—2 treatment at shoot growth stage were significantly higher than those of other treatments, but G—1 was lower than G—2, G—3 and G—4 by 70.85%, 64.37% and 39.66%, respectively. The water demand of jujube after flowering stage was increased. Stomatal conductance of G—4 was the highest of all the treatments. The highest stomatal conductance of cotton was obtained in G—2 at bud stage, after flowering, the lower irrigation quota treatments (G—1 and G—2) also had lower stomatal conductance, when it came into the later stage of growth, stomatal conductance for each treatment was significantly decreased, compared with that at the flowering stage and boll-forming stage, it was decreased by 14.34%, 31.83%, 54.23%, 43.03% and 47.71%, respectively. Effects of spacing of jujube intercropping with cotton on cotton photosynthetic rate Pn, stomatal conductance Gs, intercellular CO2 concentration Ci were mainly occurred after the period of flowering, but the effects of transpiration rate were throughout the whole growth period. Water use efficiency of cotton with different planting spacings was in decreasing order of CK—M, J—3, J—2 and J—1, and that for different irrigation quotas was in decreasing order of CK—M, G—2, G—3, G—2 and G—4. Water use efficiency of jujube with different planting spacings was in decreasing order of J—3, CK—Z, J—2 and J—1, and that for different irrigation quotas was in decreasing order of G—1, G—3, CK—M, G—2 and G—4. It was found that photosynthetic distribution based WUEPn at different growth stages was not consistent with yield based WUEyield. Cotton at bud stage had a high WUE even at low quota of irrigation, but after entering the flowering stage, WUE was closely related to irrigation quota. WUEyield of cotton for the whole growth period and WUEPn of cotton at bud stage was significantly related, WUEPn of other two growth stages had no significant correlation with WUEyield.