Silver pomfrets (Pampus argenteus) are one of the high market price among marine economic fishes, with female individuals exhibiting higher growth rates and larger body sizes. However, the process of sexual differentiation in this species remained unclear. In this study, the histological evidence of gonadal development processes before, during and after sexual differentiation was studied in silver pomfrets, revealing a duration of juvenile hermaphroditism during sexual differentiation. The individuals were further categorized into three distinct types (type A, B and C) based on the proportion of PN follicles and the presence of apoptotic bodies in their gonads. The process of sexual differentiation in individuals administered with E2 or MT revealed that individuals categorized into type A pattern exhibit a female-biased tendency and subsequently develop ovarian follicles, whereas individuals of types B and C displayed a male-biased pattern, leading to apoptosis of oocytes and contributing to the formation of testicular lobules. Additionally, the emergence of sexual size dimorphism between male and female silver pomfrets was observed prior to sexual differentiation. Our further evidence had revealed a significant increase in lipid content within the female-biased gonad and serum, as compared to that found in the male-biased samples during sexual differentiation. Moreover, we have found that lipid supply can influence the process of sexual differentiation, with fish oil leading to feminization when compared to soybean oil. In summary, the present study investigated the process of sexual differentiation in silver pomfret and provided support for the hypothesis that manipulating lipid supply can influence the sexual differentiation process and regulate the sex ratio in aquaculture.