The variation of phenotypic traits with environmental gradient can reveal the plant adapting strategies and predict reactions to future climate changes. However, it remains elusive, especially for alpine timberline tree species. To quantify the variation and explore the patterns of twig, leaf, stoma traits, and determine the scaling relationships along the topographic gradients, 576 current-year branches of Larix potaninii ssp. chinensis were collected and scaling relationships were analyzed. The results showed that the twig, leaf and stoma traits varied nonlinearly along altitudinal gradients (2900–3500 m) in both sunny and shady slopes, with a reversal point at about 3250 m, at which the optimum growth of twig length (78.53 mm), twig cross-sectional area (3.35 mm2), internode length (13.14 mm), leaf length (19.30 mm), specific leaf area (0.01 mm2mg−1), stomatal length (47.05 µm) and density (160.20 mm−2). In addition, the values of leafing intensity, leaf number and stomatal density on sunny slope, 1.52 mm−3, 88.79 and 160.20 mm−2 respectively, were higher than that on shady slope. Moreover, the relationships between leaf-twig traits were significantly correlative, and the leaf area-twig cross-sectional area and leaf intensity-leaf area scaling relationships were allometric (slope ≠ 1 or slope ≠ −1) and showed common slope with different y-intercept across altitudes and slope aspects (P < 0.01). Overall, the scaling relationships of different traits across topographical gradients were governed by functional coordination. The twig-size-leaf-size always maintains the balance between geometric dimension and mass in a certain growth rate. The inverse proportion in leaf size and number revealed its maximizing limited resource use efficiency.