Abstract: It is difficult for plants to survive and grow under the increasing stress caused by alternate dry and wet conditions in the limestone area of southwestern China where the rocky desertification has been getting worse. Arbuscular mycorrhizal fungi (AMF) have positive effects on plant growth and can increase resistance of plants to environmental stresses like drought. However, it is unclear whether AM fungi stimulate the tolerance of host plants to alternate dry and wet cycles. In this study, we took Lonicera japonica, an important native species in the karst regions of southwestern China, as our experimental material, and manipulated three factors (inoculation, water treatment, drought treatment duration) in a randomized design, to test whether AM fungus infection increases the plant’s tolerance to drought and alternate drought and wet cycles. We assessed the responses of its root length, root surface area, root diameter, and root biomass allocation and distribution to these treatments. The results showed that short periods of drought increased the root length, root surface, root volume and root biomass of non-inoculated L. japonica seedlings. Re-watering after a short drought had a positive effect on the growth of seedlings. However, under a longer drought period, all the morphological traits such as root length, root diameter, root surface area and root volume were decreased for non-inoculated seedlings, and root biomass allocation declined remarkably. Re-watering after a prolonged drought showed no positive effect on root growth of seedlings. A short drought decreased root length, root diameter, root surface area and root volume, but did not change the root biomass allocation of inoculated seedlings. Re-watering after a short drought maintained the positive effect on root growth of seedlings, possibly via the mycorrhizal vesicle structure. However, a prolonged drought caused severely negative effects on the inoculated seedlings and the compensatory growth effects vanished. The results indicated that AM fungi enhanced root growth of L. japonica seedlings both at drought and alternate drought and wet conditions in the karst area; however, this response was independent of water availability and drought duration.