Understanding the diversity of life history, life stage connectivity and population is essential to determine the spatial scale over which fish populations operate. Otolith microchemistry analysis is a powerful tool to elucidate the life history and population connectivity of fish, providing important insights to the natal origin and population structure. In this study, we used laser ablation inductively coupled plasma mass spectrometry to analyze the chemical composition of otoliths throughout the entire lifetime of endangered fourfinger threadfin species, Eleutheronema tetradactylum. We reconstructed the life history of E. tetradactylum from Southern China collected from different locations over a spatial scale of 1200 km. Sr:Ca and Ba:Ca ratios profiles from otolith core-to-edge analysis suggested two contrasting life history patterns. Based on the differences in early life stages, we identified some fish spending their first year in an estuarine environment with subsequent movement to marine coastal systems, while some fish remaining in the coastal systems throughout their entire early life history stages. The non-metric multi-dimensional scaling showed a strong overlap in otolith core elemental composition, indicating a large-scale connectivity in the life history of E. tetradactylum. The immature fish from different natal origins mixed to a large extent when they fed and overwintered in the extensive offshore waters. Clustering of near core chemistry pointed to three possible sources of nursery for the threadfin fish. This study demonstrated the diversity of life history patterns of E. tetradactylum in Southern Chinese waters. Restoration in egg and larvae densities in coastal waters and estuaries may enhance their population abundances.