Populus pruinosa Schrenk (P. pruinosa) is an important domestic forest species, only distributed in Xinjiang in China. To better protect the genetic germplasm resources of P. pruinosa populations, we study the phenotypic variations of leaf, seed, and fruit traits affected by geographical and climatic factors through investigation of natural P. pruinosa populations. Here, twenty-eight traits associated with leaf, seed and fruit characteristics were measured in the seventeen populations. The results of phenotypic variation show that leaf phenotypic traits directly exposed to the air undergo the greater morphological changes in order to adapt to changes in the external environment. The changes of phenotypic traits of different natural P. pruinosa populations can reveal different patterns of geographic variation. The phenotypic variation of P. pruinosa among populations (44.45%) was significant more than that within populations (18.14%), suggesting that the former was the main source of the total variation in phenotypic traits. The correlation analysis of phenotypic traits of natural P. pruinosa populations and environmental factors show that changes in annual average precipitation and evaporation have the most significant effects on the phenotypic traits. These results indicate that the phenotypic traits of natural P. pruinosa populations in the arid area are more sensitive to the damp environment over a long period of evolution.