Background: The secondary forests have become the major forest type worldwide, and forest gap was also a common small disturbance in secondary forests. We aimed to analyze the effects of small gap disturbance on the plant species richness of subtropical secondary forest with natural regeneration barriers and examine the relationship between soil topography and plant species in a subtropical Rhododendron secondary forest of the Baili Rhododendron National Nature Reserve. Methods: The major plant species and soil topography gradient factors of the small gaps and closed canopy (control group) were analyzed using two-way ANOVA, multivariate permutational analysis of variance, nonmetric multi-dimensional scaling, random forest, canonical correspondence analysis, redundancy analysis, and a generalized linear model. Results: Small gaps had significant impact on the distribution of soil available potassium (AK), organic carbon to total phosphorus (C/P) ratio rather than slope position for soil pH and calcium (Ca) under closed canopy. Soil pH and AK followed by total phosphorus (TP) were the most important variables explaining the spatial distributions of soil properties in both habitats. Determining the spatial distribution of individual woody plant species were soil pH in small gaps, instead of lower altitude, TP, total potassium (TK) and sodium (Na) concentrations for both habitats. Moreover, Ericaceae and Fagaceae were strongly associated with pH in the small gaps. However, there was soil Na for the herbaceous plant in the closed canopy. The species richness of woody plant species in small gaps was affected significantly by pH, soil water content (SWC), and TK, instead of soil organic carbon (SOC), SWC and C/P ratio in both habitats. Conclusions: Small gaps were not always significantly improved the composition of soil nutrients, but provided a good microenvironment for plant growth, species richness of major woody plant differed between habitats.