Soil water holding capacity is the key index of water conservation capacity of ecosystems and vital parameter of ecological service function in Nature Reserve. Four typical ecosystems including forest, shrub, bamboo, and grassland were selected in the study area of Wuyunjie Nature Reserve (WNR) of Hunan Province and soil physical properties and water holding capacity were studied through field investigation, soil sampling, and laboratory analysis. The results showed that the four typical vegetation-covered lands had greater soil organic matter content (>76 g/kg), lower bulk density (<0.85 g/cm³), and higher soil aggregate stability (stable aggregate (>5 mm in diameter) contents ranging from 22.7% to 52.3%) in the surface soil layer (0-20cm) than the local farmland, suggesting that soil structural development was generally better in the reserve area. Soil macroporosity and saturated hydraulic conductivity (K_s) in forest and bamboo ecosystems were greater than those in shrub and grassland ecosystems, which were beneficial to the rainfall transfer to groundwater. However, soil capillary porosity in shrub and grassland ecosystems were higher, indicating that more soil available water could be reserved. The gravimetric soil water holding capacity (WHC_g) in the 0-40 cm soil layer under four typical ecosystems in WNR changed in the following order: forest (83.5 mm)> bamboo (79.2 mm)> shrub (66.9 mm)> grassland (43.8 mm). However, soil available water holding capacity (WHC_a) were the following: grassland (128.7 mm)> shrub (111.6 mm)> forest (95.9 mm)> bamboo (83.9 mm). On the basis of verifying the definition of total water capacity (>0 MPa), WHC_g (0-0.01 MPa), WHC_a (0.01-1.5 MPa), and unavailable water capacity (>1.5 MPa), we recommended that WHC_g and WHC_a could be used to measure soil water holding capacity of ecosystems. WHC_g could be used to assess the capability of recharging groundwater and adjusting river flow, while WHC_a could be used to assess the potential of soil water holding capability in the ecosystems. These indexes all could be measured through soil water characteristic curves. The close relationships between soil water holding capability and water storage capacity demonstrated that, vegetation type and soil structure were of importance in water sources reserve. Forest and bamboo ecosystems, characterized by the well-developed spatial structures, had stronger capability in recharging groundwater and adjusting river flows. However, shrub and grassland, which had relatively undeveloped spatial structure, could reserve more soil available water in the ecosystems. All these were associated with the changes in soil structures. Therefore, the conservation of diverse ecosystems has crucial ecological significance in the diversity conservation of habitats and eco-environments in the WNR.