Although nucleobindin-2 (NUCB2)/nesfatin-1 has multiple biological functions, there is a scarcity of information regarding the regulatory effect of NUCB2/nesfatin-1 on lipid metabolism in mammals and fish. In order to investigate the mechanism underlying the effect of nesfatin-1 on lipid metabolism in largemouth bass (Micropterus salmoides), the sequence of NUCB2 was cloned and nesfatin-1 was expressed in prokaryotic system. Intraperitoneal injection of 5, 50 or 500 ng/g nesfatin-1 protein to determine differentially expressed genes (DEGs) in largemouth bass by transcriptomic profiling. The triglyceride and total cholesterol levels in the hepatopancreas and plasma were subsequently determined. The results showed that the NUCB2 cDNA sequence was 2015 bp in length and analyzed that NUCB2 mRNA was abundantly expressed in the hepatopancreas. RNA-seq analysis revealed that 385, 1647, and 750 genes were differentially expressed in the three groups, respectively, of which 33, 69, and 61 DEGs, respectively, were involved in lipid metabolism. GO and KEGG analysis showed that the DEGs were enriched in 24 signaling pathways related to lipid metabolism. The PPAR signaling pathway was significantly enriched following treatment with nesfatin-1. The fatty acid transport genes (ACSL, FABP3, FATP, ACBP) were significantly downregulated in the pathway (p < 0.05). Additionally, the TG (p < 0.01) and T-CHO (p < 0.05) levels in the hepatopancreas were significantly down-regulated at 50 ng/g nesfatin-1 protein injection dose, while TG and T-CHO levels in plasma were not significantly altered (p > 0.05). The present study demonstrated that at an optimal concentration, nesfatin-1 affected lipid metabolism in the hepatopancreas of largemouth bass primarily via the PPAR signaling pathway, to down-regulate the expression of fatty acid transport genes, which in turn decreased lipid synthesis in the hepatopancreas. The findings provide useful insights for further analysis of the mechanism underlying the effect of nesfatin-1, and for elucidating the regulation of lipid metabolism homeostasis in the aquaculture production of largemouth bass.