Ammonium perfluoro (2-methyl-3-oxahexanoate) (GenX), a replacement for perfluorooctanoic acid (PFOA), has been detected in multiple environmental media and biological samples worldwide. Accumulated evidence implies that GenX exposure might exert adverse health effects, although the underlying mechanisms have not been fully revealed. In this study, pregnant BALB/c mice were exposed to GenX (2 mg/kg/day), PFOA (1 mg/kg/day), or Milli-Q water by gavage from the first day of gestation (GD0) until GD21. Necropsy and tissue collection were conducted in pups at 4 weeks of age. PFOA and GenX induced similar histopathological changes in both the liver and the intestinal mucosa, accompanied by higher serum levels of alanine and aspartate aminotransferase. Moreover, the capacity of hepatic glycogen storage and intestinal mucus secretion were significantly decreased, suggesting dysfunction of liver metabolism and the intestinal mucosal barrier. A total of 637 and 352 differentially expressed genes (DEGs) were identified in the liver tissues of GenX and PFOA group, respectively. Most of the enriched pathways from the DEGs by KEGG enrichment analysis were metabolism-associated. Moreover, overexpression of CYP4A14, Sult2a1, Cpt1b, Acaa1b, Igfbp1, Irs-2 and decreased expression of Gys2 were observed in livers of GenX exposed pups, supporting the hypothesis that there was metabolic disruption. Furthermore, DNA damage and cell cycle arrest proteins (Gadd45β, p21, Ppard) were significantly increased, while cell proliferation-related proteins (Cyclin E, Myc, EGFR) were decreased by gestational GenX exposure in the pups' liver. In addition, imbalance of gut microbiota and dysfunction of the intestinal mucosa barrier might contribute to hepatotoxicity at least in part. Taken together, our results suggested that gestational GenX exposure triggered metabolic disorder, which might be responsible for the hepatotoxicity in the pups in addition to dysfunction of the intestinal mucosa barrier. This study enriches the mechanisms of GenX-induced developmental hepatotoxicity by associating metabolic disorder with intestinal homeostasis.