We describe herein a new method for covalent labeling of proteins using a complementary recognition pair of peptide tag and synthetic molecular probe. The rapid and specific covalent labeling of a tag-fused protein was achieved by the reaction on the tag site with the probe through their selective molecular recognition. The advantages of this method involve the facile functional modification and the high labeling specificity of the tag-fused protein, which are demonstrated in the labeling experiments in various conditions even inside cells.