The otolith morphology of fish species varies ontogenetically. In this study, 120 otoliths collected from the Ross Sea, the Amundsen Sea, the Weddell Sea, and the Lazarev Sea were used to analyze the morphological differences in otolith of Antarctic toothfish (Dissostichus mawsoni, TOA) across life stages by conventional measurement analysis, elliptical Fourier analysis and landmark method. The results showed that there were differences ontogenetically in otolith morphology. The shape of otolith changes from smooth and low complexity to intricate and high complexity, and the growth rate of otolith along the longitudinal axis is lower than that along the transverse axis. The characteristic parts, such as antirostrum, change significantly across life stages. Linear discriminant analysis showed the highest correct rate of classification is 85.417% from elliptical Fourier analysis, and followed by 79.167% from landmark method and 71.875% from geometric morphometrics, respectively.