Coilia nasus, an ecologically and economically important anadromous fish species in China, exhibits a typical riverine migratory life-history strategy. The Oujiang River Estuary, a representative macrotidal estuary in southern Zhejiang Province, is characterized by highly dynamic hydrological and salinity gradients, which exert significant influence on the habitat selection and life-history strategies of C. nasus. To elucidate the "habitat use history" of this species and better understand its migratory and developmental patterns, this study employed electron probe micro-analysis (EPMA) to analyze the microchemical composition of strontium (Sr) and calcium (Ca) in the otoliths of 15 C. nasus specimens collected from the estuary. The results demonstrated substantial variation in Sr/Ca ratios, encompassing low values (Sr/Ca≤3) indicative of freshwater environments, intermediate values (3<Sr/Ca≤7) corresponding to estuarine brackish waters, and high values (Sr/Ca>7) reflective of marine habitats. All otolith core regions exhibited Sr/Ca values below 3 (1.78~2.61), indicating that spawning and hatching occurred in freshwater. While all individuals exhibited an overall anadromous pattern, variations in individual migratory trajectories were evident, including the presence of a distinct population that overwinters in freshwater. Otolith Sr mapping results were consistent with those obtained from quantitative line transect analyses. Based on early freshwater life-history characteristics, individuals were categorized into two types: the short freshwater early life history type (Type SF) and the long freshwater early life history type (Type LF). Further analysis of Sr/Ca variation suggested the potential existence of three ecologically distinct population groups within the estuary. One-Way ANOVA of the freshwater coefficient (F_C) between Type SF and Type LF revealed significant differences, indicating divergent degrees of freshwater reliance during early life stages. These findings suggest that the complex and variable environmental conditions of the Oujiang River Estuary have shaped unique migratory behaviors and habitat selection patterns in C. nasus, demonstrating the species' adaptive responses to local environmental heterogeneity. This study, through otolith microchemical analysis, not only provides a detailed reconstruction of the habitat use history of C. nasus in the Oujiang River Estuary but also offers a scientific foundation for understanding its ecological traits and informing effective conservation and management strategies.