We studied the growth of roots of white mulberry (Morus alba) trees in response to different water and nutrient conditions in sets of three or five containers connected via small pipes and arranged so as to simulate the heterogeneous soil conditions associated with rocky desertification. The experiment was conducted to improve understanding of the adaptation of M. alba to this stressful environment. The trees were grown for a year under constant water and nutrient conditions in the soils within each container of any set of containers. Differences in root activity and endogenous hormones within root tips were measured at the end of the experiment. We compared four treatment groups: H (variable moisture among containers), F (variable nutrients among containers), HF (both moisture and nutrients varied among containers), and CK (non-varied control). Results showed the following: (1) Mulberry roots showed obvious hydrotropic and chemotropic growth patterns, but chemotropism did not occur in the condition of water shortage. (2) Measurement of growth indices (root surface area, total root length, number of root tips, root biomass) showed that growth status was best in group HF once the roots were able to access containers with sufficient water and nutrients, followed by group H. The indices were significantly poorer in groups F and CK. (3) The content of auxin, cytokinin, and gibberellins in roots under soil drought conditions were lower than under wetter soil conditions. In contrast, abscisic acid content and root activity were higher under soil drought conditions than under wetter soil conditions. The results indicated that water is the key factor restricting growth of white mulberry trees in areas of rocky desertification but that the trees adjust endogenous hormones in their roots to promote tropic growth and obtain sufficient moisture and nutrients over the long term. Moreover, under long-term drought stress conditions, mulberry trees retained high root activity which appears to be adaptive in that all of the trees survived.