Geometric morphometrics is a shape statistical analysis method based on Cartesian landmarks. This approach can retain comprehensive shape information of original sample, and analyze shape data along with mathematic and statistical techniques, and is therefore widely used in many fields, including fish ecology. In this review, the development, important concepts, research methods of geometric morphometrics and its research progress of application in fish ecology are briefly described. The application of this approach in the field of fish ecology can be summarized as three aspects, i.e., the effect of environments on individual development, adaptive radiation, and functional form and ecology. The results show that, in the ecological study, geometric morphometrics can reflect explicitly morphological difference and fit the subsequent data analysis, however, the theoretical research and technology development need to be improved. The approach has promising prospects in reflecting functional form and combining ontogenesis, and multi-aspect and three-dimensional shape analysis.