ABSTRACT The Chinese tapertail anchovy ( Coilia nasus ) stands as the last self‐sustaining anadromous species maintaining large upstream migratory populations in the Yangtze River basin. The migratory ecology of C. nasus remains poorly understood owing to challenges in tracing natal origins and freshwater habitat use. To address this, we developed a Sr isotope baseline ( 87 Sr/ 86 Sr) using water samples and juvenile otoliths (younger than 2 months). Distinctive 87 Sr/ 86 Sr ratios in Poyang Lake served as reliable natural markers, enabling 100% accurate identification of Poyang Lake origin freshwater‐resident Coilia brachygnathus individuals, making it possible to trace the natal origins and freshwater habitat use in Poyang Lake. However, the classification success rates of the low and middle reaches of the Yangtze River main channel, Dongting Lake and Shijiu Lake are relatively low. Otolith 87 Sr/ 86 Sr ratio analysis of adults revealed strong natal homing, with 97.7% (127/130) of specimens captured in Poyang Lake originating from Poyang Lake. The 87 Sr/ 86 Sr profiles demonstrated the diversity in the timing of their migration out of Poyang Lake, illustrating variations in life history. Three distinct life‐history categories emerged from 87 Sr/ 86 Sr profiles: long‐term residents (> 60% juveniles) exhibiting prolonged lacustrine residency, medium‐term residents transitioning to the Yangtze mainstem prior to marine migration and short‐term residents (body length, < 28 mm) demonstrating rapid freshwater outmigration. Notably, almost all juveniles completed marine transition before the first annulus formation (one exception). These findings establish critical ecological benchmarks for assessing the impacts of the construction, management and operation of the Poyang Lake Hydraulic Project on C. nasus life‐history diversity and population connectivity.