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Leaf symmetry and leaf size are explained by genetic variation between and within lineages and to a lesser extent by climatic factors, while leaf asymmetry can only be partly explained by geographic factors in Quercus aquifolioides Rehder & E.H. Wilson. Leaves are the primary photosynthetic organs of plants, and their morphology affects various crucial physiological processes potentially linked to fitness. We explored the variation in leaf morphology of an alpine oak, Quercus aquifolioides, in order to examine its relationship to genetic, geographic, and climatic factors. We conducted a genetic survey using 25 nuclear microsatellites. Based on Bayesian clustering analysis, 273 sampled trees from 29 populations of Q. aquifolioides were assigned to two lineages that correspond to the Western Sichuan Plateau-Hengduan Mountains (WSP-HDM) and Tibet geographic areas, with some individuals showing mixed ancestry. To undertake morphological analyses, we collected 1435 leaves from these trees and characterized them in terms of 13 landmarks. The metric dimensions of these leaves were digitally captured in the two-dimensional coordinates of these landmarks, then divided into leaf size and symmetric and asymmetric components of leaf shape. To analyze how different components of leaf morphology vary across lineages, we employed Procrustes Analysis of Variance (ANOVA), two-block partial least-square analysis (2B-PLS), and several other multivariate analysis approaches. We also applied distance-based redundancy analysis (dbRDAs) to explore relations between leaf morphology and genetic, geographic, and climatic factors. Multivariate analysis indicated significant differentiation in leaf symmetric shape components and leaf size between the WSP-HDM and Tibet lineages, while the mixed individuals were morphologically intermediate. The dbRDA analysis showed that most of the variation in symmetric components and leaf size was explained by genotypic effects, with the symmetric components of leaf shape being also significantly explained by geography and climate; however, variation in asymmetric components is only very weakly explained by geography. Our results demonstrated that leaf morphological variation in shape and size across Q. aquifolioides geographic range is related to both its genetic differentiation and to a lesser extent to climatic factors. We discuss how these patterns could be interpreted in terms of both geographical isolations among and within lineages, and possible adaptive responses for particular traits, in contrast to asymmetric variation.