A research on phenotypic characters of 113 individuals from seven populations of P. micranthum was investigated to reveal its variation by the methods of coefficients of variation, the nested analysis，principal component analysis，correlation and cluster analysis. The results indicated that Coefficients of variation of all characters were from 0.088-0.189; Moreover, there were the large values of variation coefficient in pedicel length, leaf length, ratio of leaf length and leaf width, length of epidermal fibers. 18 quantitative characters involved in leaf and flower traits revealed that there were only 5 characters, for instance, leaf length and its width, bract length and its width, pedicel width, which they had no significant difference at population level. Phenotypic differentiation coefficient of 18 characters varied from 2.05%-50.62%. All characters attained to a mean value of 22.02% and that suggested that 77.98% of variability came within population level. Pearson coefficient revealed that there were higher correlations not only in sepal, synsepal, dorsal width, pedicel length and ratio of leaf length and width, but also in pouch and fuit length. Nevertheless, leaf width, bract length, staminode size and synsepal height had low relevance to other characters. Seven populations were divided into two groups based on Eulidean distance cluster dendrogram. Population Yangliujin and Magu had closer relationship. Other five populations belonged to one group, among which population Douzui, Jiahanqing and Tianba were close.