Traditionally, phenotype features collection and measurement analysis in physical anthropology have relied heavily on manual measurements and observational evaluations, for which inter-observer error, and labour-intensity in large-scale sample collection present major challenges. Recently, 3D measuring technology is more and more used as a faster, more efficient and accurate human face phenotyping method which extracts more detailed human face phenotype features and characteristics those could not be captured and measured accurately by the traditional way. Based on 3D human face model, this research introduces an accurate and robust land-marking method by using 3D mesh curvature and vertexes neighborhood feature processing. With this land-marking method, the endocanthions and pronasale are located on the 3D human face mesh with accuracy higher than 98%, additionally, more human face feature points such as nasion, subnasale, left and right alares and the deepest points on the lateral side of alares are located accurately. According to these feature points located on the 3D human face mesh, an efficient quantification analysis system of observational phenotype features is established, features like asal depth, nasion height, facial flatness, etc. are measured and analyzed. In order to analyze sexual dimorphism in Modern Chinese population, phenotype features extracted from 3D human face meshs and manual morphometrics are compared and evaluated. It was found that most of facial phenotype features had gender differences in the Modern Chinese population, and nasal depth, nasion height and facial flatness present the most significant differences, with Value P<0.01 in the Z-Test. The result shows that men’s noses were larger and protruding frontwards than women’s, while women’s faces are flatter accordingly.