The shrub, leaf, and fruit traits of natural blue honeysuckle populations at different elevations were measured to explore the key factors influencing phenotypic variation as well as the intra- and interpopulation differences in phenotype. Thirteen phenotypic traits were measured at seven elevations (600-1800 m) on Changbai Mountain, China. Analysis of variance indicated that the inter-population variance accounted for 16.2261% of the total variation, whereas the intra-population variance accounted for 14.1178%. Our findings indicated that the leaf and fruit characters varied between and within populations, with the diversity between populations being greater than that within populations. The range in the coefficient of variation (11.9419%-21.7084%) suggested that the phenotypic traits varied to some extent at the species and population level and that these traits demonstrated adaptive potential. The Shannon-Wiener index indicated that the phenotypic diversity of the populations at the individual level was high. The inter-population correlation between phenotypic traits and environmental factors showed that tree height, crown length diameter, crown length diameter/crown short diameter, leaf thickness, leaf shape index, and fruit longitudinal diameter were plastic in response to environmental change. We found that inter-population variation was the main source of phenotypic variation, and the temperature changes associated with altitude primarily influenced the phenotypic changes.