Larix principis-rupprechtii Mayr is an important ecological and afforestation tree species that is distributed in North China. Unlocking the phenotypic variation of its cone is of great significance to provide insights on the production of improved varieties and the study of ecological adaptability. In this study, 12 phenotypic traits of 7,800 cones, which were collected from 13 natural populations in the entire distribution area of Larix principis-rupprechtii, were analyzed. Extensive genetic variation was observed, while the intra-population variation (45.3%) was higher than that among the populations (12.38%). The coefficient of variation on cone weight was highest with broad variation range in population, whereas the coefficient of variation on breeding scale rate was lowest. The cone weight showed very significantly negative correlation with longitude, the length of cones, the number of scales and the ratio of height to diameter were significantly negatively correlated with longitude, and the weight was also significantly negatively correlated with latitude. Principal component analysis showed that the first four principal components contributed to 84.7% of phenotypic variations. Thirteen natural populations were classified into three clusters based on Euclidean distance using cluster analysis. No significant correlation was detected between phenotypic distance and geographic distance. Collectively, this work provided information valuable on collection and utilization of excellent genetic resources of Larix principis-rupprechtii, which has implications for the production of improved varieties in the future.