Understory vegetation is an important component in most forest ecosystems. It is very important for soil and water conservation in karst region, study on understory will provide valuable information for understanding the interaction mechanism between understory flora and karst environment. Thirty-two plots were sampled in three vegetation types along with a restoration gradient (shrubland, forest-shrub transition, and mixed-species broadleaf forest) in typical karst mountains in Southwest Guangxi, China. Overstory trees, understory vascular plants, soil nutrients, and topographic factors were recorded in each 400-m2 plot. Multivariate statistics were used, including the multi-response permutation procedure (MRPP), indicator species analysis, and canonical correlation analysis (CCA). MRPP showed understory species composition significantly differed among the three vegetation types, with the greatest difference between the shrubland and the mixed forest. Twenty-one understory species were identified as significant indicator species, with 13 species being identified as indicators of the shrubland, two of forest-shrub transition, and six of the mixed forest. Light-demanding herbaceous seed plants were common in shrubland, while shade-tolerant calcicole assembled under the mixed forest. Forward selection of CCA ordination revealed that understory plant distribution was most strongly influenced by elevation, followed by soil pH, the concentration of total potassium and exchangeable calcium, slope aspect, slope degree, and the concentration of available potassium. The result reveals that vegetation types affect understory species composition by modifying understory environments. Elevation affects the spatial distribution of vegetation and soil factors, and then the understory plants. Meanwhile, soil Ca content also plays a key role in the understory species distribution. Understory diversity increased with increasing canopy structure complexity from shrubland to mixed-species forest. Thus, it is necessary to take measures to promote natural vegetation restoration and to protect the mixed forests in degraded karst areas.