Karst is one of the most important fragile ecological environments in globally terrestrial ecosystems. It is basically characterized by the dual structure of surface soil and underground karst fissures and caves, due to the long-term strong chemical dissolution of carbonate rocks. In recent years, under global climate change, the rainfall pattern in southwestern China has shown a trend of decreasing rainfall frequency and greater sub-rainfall. The karst region in southwestern China, which belongs to the subtropical monsoon climate, often suffers from more obvious alternating wet and dry conditions. The underground karst fissures and variation in the temporal pattern of regional rainfall will have a significant impact on plant growth and development in this region. In this study, in order to explore whether the seedlings of Phoebe zhennan S. Lee adjust biomass allocation and root distribution to adapt to the changing environment, we simulated different karst fissure habitats (S₀:24 cm soil; S_1/2:12 cm soil layer+12 cm karst fractured layer; S_3/4:6 cm soil layer+18 cm karst fractured layer) and different rainfall temporal patterns (I_2d:rainfall interval of 2 days; I_19d:rainfall interval of 19 days), and checked the plants biomass accumulation and allocation, root vertical distribution. The results showed that:(1) under the short-term rainfall pattern, compared with the whole soil habitat, the habitat with a small proportion of karst fissures did not affect the biomass accumulation of P. zhennan seedlings. With the thickening of karst fractured layer and the extension of the rainfall interval, P. zhennan reduced the total biomass, allocating less biomass to stems and more to roots and leaves. (2) The vertical distribution of root system of P. zhennan seedlings decreased with the deepen of soil layer, but increased the root biomass allocation ratio in the soil layer above the karst fissures, regardless of the rainfall temporal pattern. The results show that the fissures hosted soil can be a certain habitat for plants. However, with the thickening of fractured layer and extension of the rainfall interval, the fissures weaken the ability of the habitat. P. zhennan seedlings increase investment to root and leaf at the expense of stem biomass, and increase the root distribution in the interface soil layer above the fissures to ensure the maximum use of limited soil resources so as to adapt to the fissure (and arid) habitat in karst.