<p>As calcareous accretions in the inner ear of teleost fishes, otoliths accumulate abundant biological and ecological information throughout their lifetime. The microstructure of otolith is highly species-specific and has become an efficient tool in intraspecific comparisons to identify fish stocks. The inter-population variations in sagittal otolith morphology of <i>Conger myriaster</i>, a commercially important species in East Asia were analyzed, as well as the growth characteristics and population structure were also explored by otolith-based data in this study. The <i>T</i>-test results showed no significant differences between bilateral sagittas of <i>C. myriaster</i> just like most bony fishes. The distinct accumulation rates along major and minor axes brought about its elliptical shape of sagittal otolith. The fitting relationships between otolithic size and somatic growth revealed that the otolith major axis growth prioritized body weight accumulation, while its minor axis displayed more pronounced growth rate variations than body length. Principal components with eigenvalues greater than 1 were extracted, and the cumulative contribution rates reached up to 94.723% and 76.352% based on 9 shape indices and 25 Fourier coefficients, respectively, indicating that all morphometrical indicators had high information representativeness. Discriminant function scatter plots visually showed a relative independence of Dalian population, whereas the remainders were overlapped closely. Our results unveiled otolith axis-specific differential during body growth of <i>C. myriaster</i>, and demonstrated population homogeneity along the coasts of China with the exception of the Bohai Sea since its unique geographical setting.</p>