Taking the Picea schrenkiana var. tianschanica forests at three sites with different longitudes (Zhaosu, Tianchi, and Qitai) in Tianshan Mountains as the objects, the cones were collected along an altitudinal gradient to analyze the variation of their seed morphological traits (seed scale length and width, seed scale length/width ratio, seed wing length and width, seed wing length/ width ratio, seed length and width, and seed length/width ratio). All the seed traits except seed width tended to decrease with increasing altitude. The seed traits except seed wing width, seed width, and seed length/width ratio all had significant negative correlations with altitude. Seed scale length and width and seed scale length/width ratio had significant positive correlations with longitude. Seed scale length, seed scale length/width ratio, and seed wing length/width ratio had significant negative correlations with slope degree. No significant correlations were observed between the seed traits except seed wing width and the slope aspect. Altitude was the main factor affecting the seed scale length, seed scale length/width ratio, and seed wing length/width ratio.