This project comprises global proteomic and phosphoproteomic data from human intrahepatic biliary organoids derived from pediatric patients with biliary atresia (BA, n=11), choledochal cysts (CC, n=5), and histologically normal controls (NC, n=5). The data were generated by LC‑MS/MS and are organized into two subprojects: (1) global proteome quantification and (2) phosphoproteome analysis. These datasets support integrated multi‑omics investigation of fibro-inflammatory and metabolic dysregulation in BA.