Exploring how distribution patterns of understory vegetation are affected by environmental factors is of great importance for natural forest protection and biodiversity conservation. Natural and mature Excentrodendron tonkinense-dominated forests on karst terrains were studied in eight counties of Southwest Guangxi. One-way ANOVA, Pearson correlation and redundancy analysis (RDA) were used to investigate the variation in species diversity and understory structure along a gradient of environmental factors including soil, topography, canopy structure and light. The results showed that the shrub layer was dominated by Sophora tonkinensis, Schefflera heptaphylla and Ventilago calyculata, as well as seedlings of species from the tree layer, such as Excentrodendron tonkinense, Orophea anceps, Cinnamomum saxatile and Garcinia paucinervis, etc. These species mainly represented the Leguminosae, Araliaceae, Rhamnaceae, Tiliaceae, Annonaceae, Lauraceae, Guttiferae and Euphorbiaceae families. Within the herb layer, the dominant species were Nephrolepis cordifolia, Guihaia argyrata, Pseudodrynaria coronans, Microstegium vimineum, Apluda mutica and Ophiopogon bodinieri, which mainly represent the Nephrolepidaceae, Palmae, Drynariaceae, Gramineae, Liliaceae, Aspleniaceae and Dryopteridaceae families. Soil pH, soil water content (SWC), soil total potassium (TK), soil total phosphorus (TP) and slope (SLO) were the main influencing factors, respectively explaining the variation in understory species diversity by 32.3%, 16.1%, 9.7%, 8.6% and 8.6%. Shrub richness and the shrub diversity index were significantly and negatively correlated with TK, SWC, soil pH and TP, while herb richness and the herb diversity index were significantly and positively correlated with TK. Shrub density and shrub coverage were positively linked to soil pH (P < 0.05), and herb density was positively associated with SWC and TK (P < 0.05). Herb coverage was positively correlated with TP and TK, and negatively correlated with slope (P < 0.05). Soil and topography were the most important factors affecting species diversity in the understory, while canopy structure had little effect on it. Edaphic factors were found to affect understory species diversity more than topographical factors.