In this study, we investigated the phenotypic diversity of 18 characters on five main natural populations of Paphiopedilum hirsutissimum that were collected from three provinces Yunnan, Guangxi and Guizhou in China. The statistical methods used included nested variance analysis, coefficient of variation, correlation analysis, principal component analysis (PCA) and cluster analysis. The results revealed significant difference at most phenotypic traits among populations if compared to that within populations. The mean phenotypic differentiation coefficient (VST) was 75.18%, indicating that the population diversity was largely contributed by the variation among populations. The average variation coefficient of the 18 phenotypic traits was variable from 6.36%–18.51%, with a higher degree of dispersion. PCA showed that plant height, length of ovary, scape height, length of maximum leaf, diameter of flower and length of synsepal were the main sources of phenotypic variation. Pearson correlation analysis showed that plant height, width of synsepal and width of dorsal sepal were significantly or extremely significantly positively correlated with the majority of plant traits, whereas only the length of synsepal was extremely significantly correlated with geographic factors. Cluster analysis revealed three groups from the five populations, which could be explained by the geographic distribution. This study found that populations of Paphiopedilum hirsutissimum have high genetic diversity, and the variation between populations is much higher than that within the population. The phenotypic diversity indicates that wild Paphiopedilum hirsutissimum populations should be protected as much as possible. Moreover, it is recommended that germplasm is preserved in nurseries and libraries in addition to in-situ conservation, and that an artificial reproduction system is established enhance our conservation efficiency.