Karst regions represent a unique ecosystem, with its obviously discontinuous and highly heterogeneous limestone soil due to the combination of exposed rocks, tattered land surface, steep slopes, soil accumulation in depressions, and often severe soil erosion. Highly heterogeneous habitats in karst areas provide different water, fertilizer, air and space for plants, which have a significant impact on plant growth and physiology. Under the global climate change, variation in rainfall temporal pattern may further exacerbate habitat heterogeneity in karst regions. Phoebe zhennan S.Lee is an endemic, national second-class protective tree species in China. Even it only distributes in karst regions sporadically, it is still considered to be a probable suitable tree there since it can grow well between the rocks. In this study with P. zhennan seedlings as the research object, we selected two kinds of rainfall temporal pattern (I_2d :The rainfall interval is 2 days, I_19d:The rainfall interval is 19 days) and three kinds of heterogeneous habitats (S₀:all soil, S_1/2:half stone and half soil, S_3/4:more stones and less soil), to investigate the response to photosynthesis and growth. The main results are as follows:(1) under the condition of I_2d, the photosynthetic rate of P. zhennan was the largest in the half stone and half soil habitat (S_1/2), and had larger ground diameter and plant height; while under the condition of I_19d, the photosynthesis and growth (plant height and ground diameter) of P. zhennan decreased gradually with the thickening of karst fissure layer. (2) In the soil habitat (S₀), the change of rainfall pattern did not affect the photosynthesis and plant height of P. zhennan, however, in the habitat with karst fissure layer (S_1/2 and S_3/4), the extension of the rainfall interval inhibited the photosynthesis and the growth of plant height and ground diameter of, but increase the density of stomata, This inhibition or promotion increased with the thickening of the karst fissure layer. The above results show that:when the rainfall interval is short and the rainfall is relatively uniform and sufficient, a small number of karst fissures can promote the growth and photosynthesis of P. zhennan, but this effect is lost when the rainfall interval is extended. On the other hand, under the condition that the soil is thick enough, the change of rainfall time interval has no significant effect on the photosynthesis and growth of P. zhennan, but the increase of the karst fissure layer exacerbates the negative impact of the increase of the rainfall interval on the photosynthesis of P. zhennan.