In order to understand the relationship between the natural regeneration and the micro-environment of the endangered species Phoebe bournei seedlings; The research object is the regeneration individuals of Phoebe bournei natural forest with DBH<5.0 cm in Bangbei Village, Fuchuan County, Guangxi. Based on survey data of 0.64 hm2 fixed monitoring sample plots, Pearson correlation coefficient, redundancy analysis and other methods were used to analyze the relationship between seedling regeneration density and micro-environment factors of the sample plot. The results show that: (1) The largest number of small seedling recruit individuals of Phoebe bournei, the density decreased with the increase of age; Low transformation rate from seedlings to saplings, and the transformation rate from small seedlings to medium seedlings is the key stage of successful regeneration of Phoebe bournei; (2) The seedling regeneration density of Phoebe bournei was significantly positively correlated with the shrub height, the distance from the nearest parent tree, and the shrub coverage of the plot, while it was significantly negatively correlated with the light intensity and the herb layer coverage of the plot; (3) Through redundancy analysis, it can be seen that the key factors affecting the regeneration of Phoebe bournei seedlings are shrub height, the distance from the nearest parent tree, shrub coverage, the leaf area index, light, herb coverage, litter thickness, and soil salinity. Light and herb coverage are the limiting factors for the regeneration of seedlings. Therefore, reducing the light intensity, reducing herb coverage, and enhancing shrub coverage are conducive to the regeneration and development of population.