Statoliths are important hard tissues in cephalopods. Significant differences are found in the external morphology of statoliths in different groups or species. In this study, stepwise discriminant analysis was used to investigate the external morphological differences in purpleback flying squid statoliths in three different marine regions, comprising the East Indian Ocean (5° S–2° N, 82°–92° E), Central East Pacific Ocean (02°37′ S–0°59′ N, 99°44′ W–114°19′ W), and Northwest Indian Ocean (17°04′ N–17°18′ N, 61°05′ E–61°32′ E). The contours of statoliths were reconstructed visually by using Fourier analysis and the landmark method. The results obtained by stepwise discriminant analysis showed that the accuracy of identification was 84.4% for the traditional measurement method, 82.9% for the Fourier analysis method, and 87.3% for the landmark method. The contour visualization results showed that the purpleback flying squid statoliths were small in the Central East Pacific Ocean, and the curvature of the side region was the most obvious. The radian differentiation of statoliths was most gentle in the East Indian Ocean. In the Northwest Indian Ocean, the rostral region of statoliths was shorter and the dorsal region was smoother. The reconstruction results detected significant differences in the outer morphology of statoliths in different marine regions. The results obtained in this study show that all three methods are effective for identifying populations, but the landmark method is better than the traditional measurement method. The reconstruction of statolith contours using the Fourier transform and landmark methods provides an important scientific basis for conducting taxonomy, according to statolith morphology.