Intraspecific variation of organisms is of great importance to correctly carry out taxonomic work, which is a prerequisite for important disciplines in paleontology such as community paleoecology, biostratigraphy, and biogeography. However, intraspecific variation is rarely studied in ectocochleate cephalopods (ammonoids and nautiloids), in which an excessive number of taxa were established during the past centuries. Since intraspecific variation of fossilized organisms suffers from various biases (time averaging and taphonomy), an extant example is needed for actualistic comparison. We applied 3D morphometry to 93 specimens of Nautilus pompilius from three different geographic populations. This dataset was used to examine the intraspecific variation throughout ontogeny in detail. Although there are slight differences between the populations as well as some measurement biases, a common pattern of intraspecific variation appears to be present. High variation appears early in ontogeny and then decreases gradually in the following ontogenetic stages. Subsequently, the variation shows an increase again before maturity until a sharp increase or decrease occurs towards the end of ontogeny. Comparison with intraspecific variation of ammonoids and belemnites illustrated that some groups have ontogenetic patterns of intraspecific variation, which are similar to that of N. pompilius. This implies that the above-mentioned ontogenetic pattern of intraspecific variation might be common in some major cephalopod clades.