[Objective] Clarifying the reduction mechanism of arbuscular mycorrhizal fungi (AMF) inoculation in insufficiency of soil nutrient and water supply, can realize the sustainable restoration of fragile karst ecosystems. [Methods] Based on the in-situ inoculation experiment in plantations in typical karst rocky desertification areas of Shaoyang County, Hunan Province, this study collected 0-15 and 15-30 cm fine roots and 0-15, 15-30, and 30-50 cm soil samples in different slopes (upper, middle, and lower slopes), to determine the infestation and community composition of AMF and physicochemical properties. Effects of key microorganism addition on soil properties such as nutrient and water were studied. [Results] The results showed that, inoculation increased the intensity and rate of AMF infestation in roots. At the generic level, Paraglomus, Glomus, and Ambispora were the dominant genera in AMF community composition. After inoculation, changes in their relative abundances were obviously and varied in different slopes and soil layers. Simpson diversity index in 0-15 cm increased at all slopes, while that in 15-30 cm increased only at middle slope and in 30-50 cm increased at middle and lower slopes, with no significant changes; all Chao1 richness indexes increased, but differed significantly only in 0-15 cm at upper slope; Pielou evenness index increased in 0-15 cm at upper and middle slopes, in 15-30 cm at middle slope, and in 30-50 cm at all slopes, with no significant changes. Alkali-hydrolyzed nitrogen (AN) concentration decreased in different soil layers, while available phosphorus (AP) concentration decreased only in 15-30 cm. Soil organic carbon concentration decreased in 0-15 and 15-30 cm, with no significant changes. Volumetric water content increased significantly in different soil layers. Capillary pores increased in 0-15 and 30-50 cm, with no significant changes. Values of pH and exchangeable Ca2+ decreased in all soil layers, with no significant changes. The ratios of AN∶AP decreased at 0-15 and 15-30 cm, indicating that the inoculation of AMF could alleviate the restriction of soil P to some extent. Correlation and redundancy analysis among soil properties showed that the changes in microbial community composition after inoculation could directly or indirectly affect soil physical and chemical conditions such as nutrient and water. [Conclusion] The results clarify the response characteristics of soil properties to AMF inoculation in plantations of rocky desertification areas, and clear the changes in nutrient and water with showing the drivers, which is helpful to break the bottleneck of soil ecological function restoration lag and improve the service function of fragile ecosystems.