Clintonia udensis belongs to the genus Clintonia of Liliaceae, is a perennial herb with two cytotypes, the diploidy (2n = 14) and tetraploidy (4n = 28). In Hualong Mountains of Shaanxi Province, the diploidy mainly distributes at 2 450 m in the south slope, while the tetraploidy mainly grows at 1900m in the north slope, which making them as an ideal material for the study of intraspecific polyploid differentiation. In this study, based on the nutritional and reproductive system of C. udensis, we would analyze the phenotypic differentiation of different cytotypes, reveal the ecological adaptation characteristics of the two cytotypes, and provide some clues for the evolution of C. udensiss polyploid. The results showed that: (1) the fruit volume of the diploidy was the most stable (CV=0.02), and the genetic diversity of the leaf length was the highest (CV=0.85) among eleven traits. Meanwhile, the fruit volume was also the most stable one in the tetraploidy (CV=0.06), while the flower quantitative had the highest diversity (CV=0.42). (2) The average of fruit volume for the tetraploidy was significantly higher than that of the diploidy, but the average of seed number was significantly lower than that of the diploidy, and the differentiation proportion of fruit and seed volume between different ploidy types was the highest (V_st=0.69). (3) On the other hand, the genetic variation of the phenotypic traits for the tetraploidy nutritional organs was lower than that of the diploidy, and the average coefficient of variation (CV=0.16) was also lower than that of the diploidy(CV=0.44). For the reproductive system, the genetic variation of the tetraploidy was higher than that of the diploidy, and the mean variation coefficient (CV=0.30) was higher than that of the diploidy (CV=0.26). (4) According to the significant, there was a differentiation occurred in phenotype traits between the diploid and tetraploid (P<0.05). However, no significant difference was found in the reproductive system between the different ploidies (P>0.05). PCA analysis also showed significant difference between the diploidy and tetraploidy. The significant phenotypic difference of the tetraploidy would be resulted from the longterm adaptation to low altitude environment.