The effects of regulated deficit irrigation (RDI) on growth of roots and shoots of cotton plants were experimentally investigated during the growing seasons of 2013 and 2014 in pot-grown cotton (Gossypium hirsutum L. cv. Meimian 99B) under rainproof shelter condition in Huang-Huai-Hai Region of China, aiming at offering theoretical basis for the establishment of RDI model for water-saving, high yield, high quality and efficiency of cotton crops. A two-factor randomize-block design was applied. The first factor was different growth stages of water deficit, including seedling stage (I), budding stage (II), flowering and boll-setting stages (III) and boll-opening stage (IV). Another factor was different degrees of water deficit, which were three levels controlled by soil relative water content, including light deficit (L), moderate deficit (M) and severe deficit (S) at stages of I to IV, corresponding soil relative water content were controlled at 60%~65% FC (Field capacity), 50%~55% FC and 40%~45% FC, respectively. Totally 12 water deficit treatments with six replicates were designed and applied. Additionally, an appropriate irrigation treatment (with soil relative water content controlled at 60%~70% FC at seedling stage, 60%~70% FC at budding stage, 70%~80% FC at flowering and boll-setting stages and 60%~70% FC at boll-opening stage) during the whole growing season was designed as control (CK) with 24 replicates. Root system parameters, such as root dry weight, root weight density and total shoot dry matter weight were measured synchronously in all treatments during water stress period and after re-watering, respectively. The results indicated that there were differences in effects of RDI on growth of roots and shoots in cotton due to both phenological stages and degrees of water deficit. Although water deficit didn’t change the original trend of root growth in cotton, the growth rate of root was promoted. The growth of root was promoted significantly during moderate water deficit (50%~60% FC) at some growing stages, and there was a ‘super-compensation effect’ in root growth or the effect on delaying senescence of root after re-watering, and a higher ratio of root to shoot (R/S) was still retained at later stage of cotton growth. Therefore, it was indicated that moderate water deficit was suitable irrigation treatment for coordinating the relation of root and shoot growth of cotton. The results suggested that RDI should be adopted as an effective approach in regulating the growth of root and shoot in cotton plants.