The yellow drum (Nibea albiflora), a pivotal species within the Sciaenidae family, is economically important in the mariculture along the coastal regions of China. A comprehensive understanding gonadal maturation and spawning processes is crucial for seed production in the artificial propagation of yellow drum. This study investigates serum hormonal fluctuations, gonadal histological features, sex hormone receptor gene expression, and intestinal microbiota composition in both male and female yellow drum during the reproductive season. Twenty individuals were sampled from reproductive stages IV, V, and VI, respectively. During the spawning season, no significant differences were observed in the levels of PROG, E2, and 11-KT across different stages, in both males and females, with no significant sex-based differences. Subsequent analysis indicated a significant upregulation of fshr, lhcgr, and esr expression in the ovary during spawning stages. In contrast, within the testis, the expression levels of fshr, ar, and esr remained relatively constant across different stages, whereas lhcgr expression was markedly higher during the spawning stages compared with prespawning and post-spawning stages. Analysis of intestinal microbiota revealed a predominance of Bacteroidota, Firmicutes, and Proteobacteria, with no significant sex differences. At the class level, the abundances of Alphaproteobacteria, Gammaproteobacteria, and Bacilli exhibited significant fluctuations during the spawning and post-spawning stages in both sexes. At the genus level, g_Muribaculaceae and g_Bacteroides were abundant during spawning stages in both sexes. A Mantel test showed significant positive correlations between PROG levels and the abundances of g_Bacteroides in males. In females, PROG levels were positively correlated with the abundance of g_Prevotella. These findings enhance our understanding of the interplay between reproductive biology and the biological functions of intestinal microbiota in yellow drum broodstock during the reproductive season, thereby laying a foundation for the development of artificial propagation technology in this species.