Coilia nasus belongs to Clupeiformes, Engraulidae, Coilia, which is a commercially valuable fish in China. Otoliths (sagittae, asteriscus, or lapillus) are complex tissue structures with calcium carbonate (CaCO₃) as the main component, and their shapes vary markedly depending on the species and population. Because sagittae (saccular otoliths) are the largest and present the most significant interspecific variation among the three pairs of otoliths, thus they are the most used in research. To compare with traditional morphological surveying methods, geometric morphometric methods transform qualitative analysis into quantitative analysis. Especially, landmark-based geometric morphometric analysis is attracting more and more attention in recent years and has been applied to a variety of fields of fish otolith investigation. In order to understand the variation in the otolith shape of C. nasus (including the long supermaxilla and short supermaxilla C. nasus ecomorphotypes, the latter was once named C. brachygnathus) populations from different sites (i.e., Xieshan site of Hukou County, Liaozuitou site and Huoyanshan site of Lushan City, Piaotou site of Yongxiu County) in northern area of the Poyang Lake and reveal their population connectivity, landmark-based geometric morphometric analysis was used in the present study. The otolith morphometric characteristics were documented with relative warp principal components analysis, discriminate analysis, cluster analysis, and further visualizing grid deformation by thin plate spline. The results showed that landmarks in the sulcus had the main contribution (77.9%) in explaining the primary source of otolith morphometric variation. Discriminate analysis of relative warps obtained 100% classification success for the variation between long supermaxilla and short supermaxilla C. nasus for the first time, demonstrating the tremendous difference in geometric morphometrics between the two ecomorphotypes. Viewing from long supermaxilla C. nasus, discriminate analysis showed that the highest identifying accuracy (95%) was found for the fish population from the Liaozuitou site, followed by those populations from the Huoyanshan site (90%), Piaotou site (55%), and Xieshan site (50%). Cluster analysis indicated that the relative closer distance could be found among the populations from Huoyanshan, Xieshan and Piaotou sites than that population from Liaozuitou site. The present study first discovered the distribution of long supermaxilla C. nasus in waters of the Liaozuitou, Piaotou and Xieshan site. It was believed that the long supermaxilla C. nasus from the Liaozuitou site might be a relatively independent population, while certain connectivity could be available among the remaining populations of this ecomorphotype from other sites in the northern area of the Poyang Lake. By analysing variation in the otolith shape of C. nasus from different sites, the present study interprets population connectivity in corresponding areas in the Poyang Lake. It possibly provides scientific basis and theoretical support for fishery management and conservation of C. nasus.