Elderly people show a decline in the ability to decode facial expressions, but also experience age-related facial structure changes that may render their facial expressions harder to decode. However, to date there is no empirical evidence to support the latter mechanism. The objective of this study was to assess the effects of age on facial morphology at rest and during smiling, in younger (n = 100; age range, 18–32 years) and older (n = 30; age range, 55–65 years) Japanese women. Three-dimensional images of each subject’s face at rest and during smiling were obtained and wire mesh fitting was performed on each image to quantify the facial surface morphology. The mean node coordinates in each facial posture were compared between the groups using t-tests. Further, the node coordinates of the fitted mesh were entered into a principal component analysis (PCA) and a multifactor analysis of variance (MANOVA) to examine the direct interactions of aging and facial postures on the 3D facial morphology. The results indicated that there were significant age-related 3D facial changes in facial expression generation and the transition from resting to smiling produced a smaller amount of soft tissue movement in the older group than in the younger group. Further, 185 surface configuration variables were extracted and the variables were used to create four discriminant functions: the age-group discrimination for each facial expression, and the facial expression discrimination for each age group. For facial expression discrimination, the older group showed 80% accuracy with 2 of 66 significant variables, whereas the younger group showed 99% accuracy with 15 of 144 significant variables. These results indicate that in both facial expressions, the facial morphology was distinctly different in the younger and older subjects, and that in the older group, the facial morphology during smiling could not be as easily discriminated from the morphology at rest as in the younger group. These results may help to explain one aspect of the communication dysfunction observed in older people.