The present disclosure relates to a method for in vivo targeting of a nanoparticle via bioorthogonal copper-free click chemistry, more particularly to a method for in vivo targeting of a nanoparticle, including: injecting a precursor capable of being metabolically engineered in vivo when injected into a living system and having a first bioorthogonal functional group into the living system; and injecting a nanoparticle having a second bioorthogonal functional group which can perform a bioorthogonal copper-free click reaction with the first bioorthogonal functional group attached thereto into the living system.In accordance with the present disclosure, accumulation of nanoparticles at a target site in a living system can be increased remarkably and the biodistribution of the nanoparticles can be controlled since the nanoparticles bound to a cell surface are taken up into the cell with time.