The Yangtze sturgeon (Acipenser dabryanus) has recently been declared extinct in the wild, and artificial breeding is the only means to protect its germplasm resources, but it has difficulty in weaning (from live prey to artificial food). In this study, we first performed a histological observation, enzyme-activity determination, and transcriptome sequencing on the livers of juvenile Yangtze sturgeons, and we then cloned five critical genes of lipid metabolism according to the transcriptome-sequencing results. We designed a weaning experiment to analyze their expression levels during weaning. The results showed that the density of hepatocytes and the transaminase activity of the juveniles failed to wean. The differentially expressed genes were enriched significantly in the pathways involving steroid synthesis, amino acid metabolism, and pancreatic secretion. It was found that the mRNA level of the fatty acid-synthesis gene decreased, and the mRNA level of the lipolysis gene increased significantly during weaning. The results of this research indicated that weaning could affect the liver health of Yangtze sturgeon, and it could affect the liver lipid metabolism by inhibiting fatty acid synthesis and promoting lipolysis. This study enhances our understanding of the impact of weaning on the lipid metabolism in fish.