Phenotypic variation within a species can be associated with varying environmental conditions in their habitats. Understanding the variations in species’ phenotypes helps to understand their resource utilization and ecological niche. The jumbo squid, Dosidicus gigas, is a keystone species of the Eastern Pacific Ocean, which is widely distributed and exhibits large phenotypic variation under environmental influences. To investigate whether different environmental conditions lead to morphological changes in the beak of D. gigas, the animal’s important feeding apparatus, a total of 244 D. gigas’ beaks were collected from the eastern equatorial Pacific Ocean from Jun to August in 2017, 129 and 115 specimens were from the western and eastern waters of the Galapagos Archipelago, respectively. Traditional morphometrics and geometric morphometrics methods were applied to quantify the external morphology of the beak. A total of twelve external morphological parameters were measured through traditional morphometrics, and twenty landmarks were set on the one-side image of upper and lower beaks and digitized for geometric morphometrics analysis. The results showed that 11 external standard morphological parameters of beaks were significantly different between different cohorts except for upper hood length (UCLs) (P<0.05). Although the coefficients of difference were all less than 1.28. Geometric morphometric analysis showed significant differences (P<0.001) in the size and shape of upper and lower beaks between the two cohorts, with different allometric growth patterns. The morphological differences were mainly reflected in the rostrum and lateral wall of the upper beak, and the rostrum and wing of the lower beak. Stepwise discrimination analysis based on land-mark geometric morphometrics showed high success rates for both upper and lower beaks, which were 89.61% and 85.88%, respectively. D. gigas from the eastern waters had smaller beaks with more curved and sharper rostrum, larger lateral walls, and wider but shorter wings compared to those from the western waters, which may be attributed to the environmental conditions and food types of the habitat. Such resource allocation-related phenotypic plasticity could be considered as a response to the environmental characteristics of their habitats, which may likely facilitate their survival.