Great challenge in agricultural production is how to harvest more with less water consumption. Improvement of water use efficiency (WUE) for plant itself becomes increasingly more important. Root system is essential to uptake water from soil for plant growth. However, it is still a divergent topic about the regulating mechanism between root morphological variations and shoots water consumption. To clarify a relationship between WUE change and root morphological characteristics further under water deficit and understand the adaptive traits to drought stress of root morphological components, the response of biomass, water dissipation and root morphology, including root length, root surface-area, root volume, basal diameter of main root to the continual drought stress conditions were studied in potted one- and two-year old alfalfa (cultivars: Long-Dong and Algonquin). Three levels of soil moisture including (75±5)%, (55±5)% and (35±5)% of field capacity were controlled with weighing method. The plants grown in rain-proof shed were irrigated by using tap water. Tests were carried out at branching and anthesis stages of one- and two-year old alfalfa plants. The results show that root morphology of alfalfa changed remarkably among plant age, harvest times and cultivars under water stress. The inhibition of main root elongation and the enhancement of lateral roots and total root elongation were stimulated by drought stress, demonstrated by enlarged root surface area and increased numbers of lateral roots (≥1 mm), with thinner main root and declined root biomass. All these root morphological changes，which differ among different seasons, harvest times or cultivars, increasing in adaptation to drought conditions is limited. On the other hand, the biomass and water dissipation amounts declined and differed with the change of season, biomass harvesting or cultivar when subjected to drought stress. Moreover, there was a significant positive correlation between root morphological characteristics and WUE, which indicated that root weight had largely effected on WUE. Therefore, the increase of WUE under water stress depended on the root morphology, including total root length, root biomass and root/shoot ratio etc., and canopy water consumption. Alfalfa tolerance to drought stress was stronger compared with two-year old plants than one-year old ones, with the first harvest and the second than third harvest, with Long-Dong than Algonquin. The adaptive changes of root morphology are the main strategies to endure drought stress in alfalfa. In general, this study explored the adaptive mechanism to drought and improvement of WUE in alfalfa.