Abstract: To reveal the variation degree and variation regularity of natural peony populations in northwest Yunnan, we used 12 morphological indexes to study the phenotypic diversity of 18 natural populations of Paeonia suffruticosa. The results showed that there was a wide range of variation in the phenotypic traits of P. suffruticosa in northwest Yunnan, the variation coefficient of the 12 traits among the populations was 16.65%- 107.78%. The average coefficient of variation among populations was 38.44%. Among the 18 populations studied, the variation of Ninglang County Township Labo population was the smallest, the coefficient of variation was 25.02% ; followed by Yulong County Dapingba population, the coefficient of variation was 26.68%; the variation of Liming Line population was the highest, the coefficient of variation was 50.86%. There were abundant phenotypic diversities among the populations and within the populations in northwest China. The mean phenotypic differentiation coefficient of 12 phenotypic traits was 98.51% , the variation among populations (48.87%) was greater than that within populations (0.59%), indicating that the variation among populations was the main source of phenotypic variation. The canonical correlation analysis between phenotypic traits and geographical factors showed that, the gradient could be interpreted in positive direction of single pod length (y11), pedicel length (y8), petiole length (y4), total number of pods (y10); the gradient could be explained in negative direction of pod width (y12), number of pods (y9), plant height (y1). The results of cluster analysis showed that the variation of phenotypic traits among populations of P. suffruticosa was discontinuous.