Larix chinensis is a timberline tree species in the Qinling Mountains, and its fruiting characteristics (i.e., seed and cone characteristics) can affect migration and also distribution patterns of the timberline. We tested the differentiation between southern and northern slopes in different communities by field investigation of the cones and seeds characteristics of L. chinensis in Qinling Mountains. We then calculated the variations of cones and seeds between slopes and among populations using One-way ANOVA and multiple comparison, and analyzed the resources of difference using coefficient of phenotypic variation and phenotypic differentiation (Vst), and calculated the relationship between the cones and seeds and environmental factors using Pearson correlation and redundancy analysis (RDA). (1) We found no significant change in cones and seeds characteristics between plants in the southern and northern slopes. The northern slope plants featured a significant variation in all cones and seeds characteristics among different populations, whereas in the southern slope, only cone weight and seed number per cone differed among different populations. (2) Phenotype variation and differentiation was larger in the southern than northern slope and the Vsts in both slopes were <0.5, so the cones and seeds characteristics varied mainly within populations. (3) We found a negative correlation between altitude and weight, length, and width of cones. As well, the mean correlation between altitude and fruiting characteristics was maximum (r=-0.475), followed by soil K, slope, pH, soil N, organic matter, soil P and gradient. Redundancy analysis showed that the fruiting characteristics were largely affected by altitude, slope and soil K. These results may be helpful to explain the factors limiting the distribution of L. chinensis, providing theoretical evidence for management and protection.