To study the intraspecies taxonomy of the Western honeybee (Apis mellifera), geometric morphometrics analyses can now replace the standard morphometry method, yet its availability for microtaxonomy of the Asian honeybee (Apis cerana F.) has not been reported. In order to assess effectiveness of geometric morphometrics analyses using the forewing in the microtaxonomy of the Asian honeybee, 180 individual worker bees were sampled from three sample sites, Jilin, Hainan, and Shaanxi, representing different habitats for A. cerana within China. Bees were analyzed by discrimination analysis using three methods: (1) standard morphometry method with 33 traditional characters, (2) simplified standard morphometry method with only 11 wing vein angles, and (3) geometric morphometrics analyses with 18 wing vein junctions. The results revealed that geometric morphometrics analyses could reflect the variability information of the forewing vein structures of A. cerana. Morphological differentiation at the three sample sites was identified. Cross-validation indicated the percentage of individuals falling into each sample site, were 98.3%, 95.0%, and 88.3% for Jilin, Hainan, and Shaanxi, respectively. Geometric morphometrics analyses produced classification results similar to those produced using the standard morphometry method, and it was superior for presenting the wing vein variability information compared to the simplified standard morphometry method. Therefore, we conclude that geometric morphometrics analyses could be efficient and effective in the microtaxonomy of A. cerana. Furthermore, geometric morphometrics is a potential method for resolving A. cerana subspecies classification issues.