As a key metabolic function of the liver, the hepatic biotransformation process can alter the predesigned surface chemistry of nanoparticles in vivo, leading to hampered functionality and targeting ability. However, strategies to modulate the hepatic biotransformation of nanoparticles have been rarely explored. Herein, using indocyanine green (ICG)-conjugated gold nanoparticles that target liver hepatocytes as a model, we showed that merely changing the metal-ligand bond from gold-sulfur (Au-S) to gold-selenium (Au-Se) completely reshaped the hepatic biotransformation profiles of the nanoparticle as well as its targeting and transport behaviors in vivo. Compared with those of Au-S bond, Au-Se bond markedly slowed down nanoparticle biotransformation in liver sinusoids, enhanced ICG-mediated nanoparticle targeting to hepatocytes by 15-fold, and also altered nanoparticle intrahepatic transport, distribution, and clearance pathways. Moreover, we demonstrated that Au-Se bond could improve the active targeting of gold nanoparticles to hepatic tumors by reducing liver biotransformation-induced dissociation of targeting ligands. These discoveries not only deepen our understanding of nanoparticle biotransformation in the liver but also offer a strategy to overcome the biochemical barrier of hepatic biotransformation, providing guidance for the design and engineering of related nanomedicines by tuning their in vivo biotransformation profiles.