To explore the effect of drought stress on main colored cotton traits and the water use efficiency (WUE) mechanism, we performed the experiments with split-plot design, irrigation amounts (normal irrigation, stress irrigation, and no irrigation) were taken as the main-plots, and seven colored cotton cultivars were used as the sub-plots. The results showed that the boll number per plant, weight per boll, plant height, leaf number, number of fruiting branch, harvest index, number of fruit nodes, seed index, stem diameter, internode length of fruit branches and main stem reduced, but the lint percentage increased under drought stress. When the irrigation amount reduced by half, all cultivars yield decreased, there was significant difference between normal irrigation and no irrigation (P<0.05). There also existed significant difference in seed cotton yield among cultivars (P<0.05), the yield reduction of brown cotton cultivar was higher than that of green cotton cultivar. Under normal irrigation, the WUE of white cotton was higher than that of green cotton and brown cotton; there was no significant difference in WUE between brown cotton and green cotton. Under drought stress, the WUE of brown cotton was higher than that of green cotton. So WUE is related to leaf number, the boll number per plant, number of fruiting branches, number of fruit nodes, plant height, harvest index, weight per boll, length between fruit branches and main stem, seed index, the stem diameter, and lint percentage.