To analyze the difference of trace elements in the nuclear part of eye lenses in different sea areas and test the performance of the microelements in the identification of geographical population of Dosidicus gigas, the research samples were taken from China’s ocean-going squid fishing boats in Ecuadorian, Peruvian and Chilean exclusive economic zones (EEZs) in the southeast Pacific Ocean in 2015 and 2017. The trace elements of eye lenses were determined to study as the population origin by applying the stepwise discriminant analysis, etc. The results showed that the trace elements in the nuclear part of eye lenses were significantly different among the three regions from the Ecuadorian, Peruvian and Chilean EEZs except for Al²⁷ and Si²⁹. The results of stepwise discrimination showed that the trace elements in the nuclear part of the eye lenses could be used to identify different geographical populations of D. gigas, and the overall discrimination success rate was 69.2%. The discrimination success rates of Ecuador, Peru and Chile were 87.0%, 70.0% and 52.0%, respectively. If the samples of the two regions from the Peruvian and Chilean EEZs were combined and then judged with Ecuador, the overall success rate rose to 89.7%, compared with 95.70% and 87.30% off the coast of Ecuador, Peru and Chile, respectively. Mg²⁵ can be used to identify D. gigas from Ecuador with Peru and Chile, while Cu⁶³ can identify Peruvian and Chilean. The high rate of mis-classification between Peru and Chile indicated that the two may belong to the “Southern Hemisphere” population, while Ecuador may be independent of the “Southern Hemisphere” and “Northern Hemisphere” populations due to different marine environments.