Abstract: In this paper, the regolith of limestone rock and basalt with different vegetation growth in the same climate zone of Kunming area is taken as the research object, and the micro-morphological characteristics are compared and analyzed by using microscopic observation and image analysis processing technology. The results show that there is obvious inheritance between limestone and basalt regolith and their respective bedrock, which is mainly manifested in that the skeleton particles in each layer of basalt regolith contain a large amount of plagioclase, while the skeleton particles in each layer of limestone regolith only contain quartz, indicating that the limestone regolith and basalt regolith are not the same kind of matter. Layer A(topsoil layer) of limestone regolith presents cracked microstructure, with a total porosity of 15.85%, and the main type of pores is aeration pores. Layer B(core soil layer) presents block microstructure, with a porosity of only 6.48%, and the main type of pores is ineffective pores. Layer A(topsoil layer) of basalt regolith presents spongy microstructure with a total porosity of 28.29%, most of which are aeration pores, and layer B(core soil layer) presents composite microstructure of pores and channels with a porosity of 9.53%, mainly capillary pores. The effective water content of limestone regolith and basalt regolith has a positive correlation with capillary pores and aeration pores, and a negative correlation with ineffective pores. These studies have outlined a new way for the theoretical study of bedrock controlling the production of overlying vegetation, that is, bedrock can affect its effective water content by controlling the microstructure of regolith, thus leading to the phenomenon that even under the same climatic conditions, the production of overlying vegetation in different bedrock areas may have a large difference.