The feeding organ of cephalopod species, the beak, can be used to reveal important ecological information. In this study, geometric morphometric approaches were employed to investigate the phylogenetic relevance and classification effect of beak lateral profile shape. The two-dimensional beak morphologies of 1164 pairs of 24 species from 13 genera and five families were constructed, and their evolutionary relationships and taxonomic status were confirmed using geometric morphometrics and molecular biology approaches. We also assessed the phylogenetic signals of beak shape. The analysis results show shape variation in the beak mainly in the rostrum, hood, and lateral wall. The overall shape parameters (all PCs) of the upper and lower beak are more useful for species identification. The shapes of the upper and lower beak show a strong phylogenetic signal, and the phenogram based on the beak shape basically reflected the families' taxonomic positions. We also hypothesized that the shape variation in the beaks of cephalopods may be ascribed to genetic and environmental differences. In summary, beaks are a reliable material for the classification of cephalopod species. Geometric morphometric approaches are a powerful tool to reveal the identification, phylogenetic relevance and phenotypic diversity of beak shape in cephalopods.