Facial morphology, the most conspicuous feature of human appearance, is highly heritable. Previous studies on the genetic basis of facial morphology were mainly performed in European populations. Applying a proven data-driven phenotyping and multivariate genome-wide scanning protocol to the largest collection of 3D facial images of an East Asian population to date, we identified 244 leading variants associated with normal-range facial variation, of which 130 are novel. A newly proposed polygenic shape analysis indicates that the effects of the variants on East Asian facial shape can be generalized into the European population. Based on this analysis, we further identified 13 variants mainly related to differences between European and East Asian facial shape. Natural selection analyses suggest that the difference in European and East Asian nose shape is caused by a directional selection, mainly due to a local adaptation in Europeans. Our results expand the knowledge of human facial genetics and illustrates for the first time the underlying genetic basis for facial differences across populations.