Plant functional traits are the measurable characteristics of plants which are formed by long-term adaptation to habitat environmental conditions. The characterization of plant functional traits is mainly influenced by both the plants specific genetic basis and the shifted environmental factors. Qilian Mountains, with an elevation ranging from 2000 to 5000 m, is one of the major mountains in the dry land in Northwest China, where naturally distributed more than 10 kinds of woody plants such as Picea crassifolia and Juniperus przewalskii on the northern slope. It is of great academic and practice significance to understand the acclimation strategy and the vertical distribution pattern of alpine woody plants by deeply investigating the woody plant functional traits variation and the behind driving mechanism along with the altitude gradients in the Qilian Mountains. In the present study, we investigated 11 naturally distributed woody plant species along with the altitude in the Qilian Mountains, which included 9 shrub species (Potentilla fruticosa, Potentilla glabra, Cotoneaster multiflorus, Ilex pernyi, Salix gilashanica, Caragana jubata, Lonicera hispida, Spiraea alpine, and Berberis diaphana, respectively) and 2 tree species (Picea crassifolia and Juniperus przewalskii, respectively). A total of six plant functional traits of shoot and leaf were investigated in this study, and which include woody density, huber value, leaf area, leaf dry matter content, leaf water content, and specific leaf area, respectively. The results showed that:(1) woody density, huber value, leaf water content, and specific leaf area of shrub species were significantly greater than those of tree species, and leaf area and leaf dry matter content of shrub species were significantly lower than those of tree species. (2) Woody density and leaf dry matter content declined significantly along with the altitude gradients increased, and the other functional traits changed insignificantly along with the altitude gradients increased. (3) Growing-season air temperature was positively correlated with leaf dry matter content, and was negatively correlated with huber value and leaf water content; however, non-significant relationships between growing-season precipitation and plant functional traits were found. The results showed that tree and shrub plants adapted to the alpine habitats by adopting different branch and leaf resources utilization strategies; the decreasing structure carbon investment with the altitude gradients increased possibly has limited the upshift of alpine plants; the growing-season air temperature was one of the key environmental factors tuning woody plant functional traits variation pattern along with the altitudes gradients but could not explain all the variance.