Abstract: Larimichthys crocea is an economically important aquaculture species in China, with the Naozhou population gaining increasing attention amid the development of offshore and deep-sea aquaculture in the South China Sea. We examined the wild Naozhou large yellow croaker (Larimichthys crocea) collected from the Xuwen coast, with gas chromatography (Internal standard method) to determine muscle fatty acid composition across different developmental stages. By integrating multivariate statistical analyses with fatty acid trophic marker approaches, we systematically investigated the ontogenetic variations in fatty acid composition and their implications for feeding structure and trophic niche. A total of 17 FAs were identified from 32 individuals, with polyunsaturated fatty acids (PUFA) accounting for the highest proportion (50.81%), followed by saturated fatty acids (SFA, 35.18%) and monounsaturated fatty acids (MUFA, 14.01%). The ΣPUFA/ΣUFA ratio and n3/n6 ratio were 1:1.28 and 5.66:1, indicating high nutritional quality of muscle lipids. SFA and MUFA were highest in early development (Stage I), declined at mid-development (Stage III), and rose again in later stages, whereas PUFA peaked at mid-development and subsequently declined. Fatty acid difference analysis reveals that variations in fatty acid composition were most pronounced during the juvenile stages (Groups I and II) and the sub-adult stage (Groups II and III), whereas differences diminished as individuals reached maturity (Group IV). Among the fatty acids examined, unsaturated fatty acids, including C16:1n7, C20:1+C22:1n9, C18:1n9, C20:4n6 (ARA), C20:5n3 (EPA), and C22:6n3 (DHA), were the primary contributors to the observed stage-specific differentiation. Their relative abundances exhibited distinct ontogenetic patterns, reflecting shifts in dietary sources and nutritional requirements throughout the growth period. Among trophic-marker fatty acids, C22:6n3 (DHA) peaked at intermediate stages and then decreased; C20:5n3 (EPA) displayed a dynamic variation; C18:1n9 and C20:4n6 (ARA) increased consistently with development; and copepod markers (C20:1 and C22:1n9) were relatively more abundant in juveniles. Fatty acid biomarker analysis indicates that the Naozhou population of L. crocea likely relied primarily on dinoflagellate-(Indicated by DHA) and diatom-based (Indicated by EPA) primary production pathways, together with zooplankton and benthic pathways (Mediated by C18:1n9 and ARA). In contrast, the contributions from copepod-, bacterial-, and terrestrial plant-derived pathways were relatively minor. This study thus provides a solid foundation for optimizing feed formulation and nutritional management of L. crocea in deep-sea mariculture in the South China Sea.