ABSTRACT The Yangtze finless porpoise (YFP) is a critically endangered freshwater cetacean endemic to China. Understanding seasonal breeding patterns is critical for the effective conservation of critically endangered species. The current study was designed to examine the function and taxonomic characteristics of fecal microbiota and their metabolites in male captive YFPs during both nonbreeding (NB) and breeding (B) seasons, analyzing 20 fecal samples using both UHPLC–MS/MS and 16S rRNA gene sequencing approaches. The present study revealed that Firmicutes were increased in the NB season, while Actinobacteria, Proteobacteria, and Fusobacteriota were increased in the B season at the phylum level. At the genus level, Paeniclostridium , Clostridium_sensu_stricto_13 , and Mycobacterium were increased in the NB season, while Romboutsia , Plesiomonas , and Cetobacterium were increased in the B season. LEfSe analysis revealed that Staphylococcus , Comamonas , and Tetrasphaera were significantly increased in the B season, while the genus Terrisporobacter was substantially increased in the NB season. The fecal metabolome undergoes significant changes during the B and NB seasons, altering metabolic pathways such as phenylalanine metabolism, protein digestion, taurine and hypotaurine metabolism, lysine degradation, tryptophan biosynthesis, tyrosine metabolism, and bile secretion. Moreover, there was a significant correlation between the fecal metabolome and microbiome in the captive YFPs in the B and NB seasons. This study explores the impact of seasonal reproduction on gut microbes and their metabolites, providing insights into animal seasonal reproductive behavior and providing a theoretical basis for studying gut microbiota and metabolites in cetaceans, both in captivity and in the wild.