This research, conducted at the National Field Science Observation and Research Station of the Aksu Farmland Ecosystem in Xinjiang, was performed to partition evapotranspiration components, identify the main water absorption depth, and quantify the contribution of soil water at different depths during different growing stages of cotton by combining hydrogen and oxygen stable isotopes and the MixSIAR model. The results indicated that evapotranspiration in the seeding stage, bud stage, flowering and boll stage, boll opening stage, and harvesting stage were 88 mm, 137 mm, 542 mm, 214 mm, and 118 mm, respectively, and the corresponding transpiration accounted for 51%, 82%, 88%, 85%, and 72% of evapotranspiration. With the development of cotton roots, the water absorption depth gradually increased, and the main absorption depths in the late bud stage, mid flowering and boll stage, late flowering and boll stage, boll opening stage, and harvesting stage were 0–20 cm, 40–60 cm, 60–80 cm, 80–100 cm, and 0–20 cm, respectively, with corresponding contributions of 35.4%, 40.9%, 27.7%, 29.9%, and 22.5%. Our results can provide a theoretical foundation for the accurate irrigation management of cotton fields.