To ensure the continual growth of mulberry at inferior sites in the area of the Three Gorges Reservoir, an analysis of soil structure stability and water-retention properties was conducted in 4 habitats defined as having stony, skeleton, gravelly and disturbed soils in this paper. Furthermore, the various soil factors acting as obstacles and the ways to improve habitats were discussed. The results showed that: (1) Significant differences (p＜0.05) were found in soil physical properties at the different habitats, and the order of soil bulk density was skeleton soil (1.30 g/cm3)＞stony soil (1.23 g/cm3)＞gravelly soil (1.12 g/cm3)＞disturbed soil (1.08 g/cm3); The sand grain content was in the same order; (2) Resistance to seasonal drought was greatly different among these habitats, and soil total storage capacity was in the order of stony soil (97.185 mm)＞gravelly soil (81.139 mm)＞disturbed soil (66.958 mm)＞skeleton soil (47.353 mm). Moreover, the maximum available capacity was stony soil (54.140 mm)＞gravelly soil (47.552 mm)＞skeleton soil (36.399 mm)＞disturbed soil (11.705 mm); (3) The soil anti-erodibility index (ASI) for different habitats was in the order of skeleton soil (4.57)＞stony soil (2.44)＞gravelly soil (2.36)＞disturbed soil (2.31). Correlation analysis indicated that soil stability was significantly or highly significantly positively correlated with sand content, was highly significantly negatively correlated with powder and clay content, and was not significantly correlated with soil porosity; (4) The soil factors considered as obstacles for mulberry were different in different habitats; soil amendments could be used to increase the soil permeability in gravelly soil habitats, water-retaining agents could be added to improve the soil available capacity in disturbed soil habitats, and nitrogen-fixing plants and green manure could be planted/added to increase soil nutrients in stony and gravelly soil habitats.