Human exposure to widespread furan-containing compounds (FCCs) has drawn much attention due to the high risk of their toxicities. Identifying adducted proteins resulting from the metabolic activation of FCCs is the core to learning the mechanism of FCCs' toxic action. We succeeded in establishing a metabolic activation-based chemoproteomic platform to map FCC-derived protein adducts in cultured primary hepatocytes treated with FCCs and to pinpoint the modification sites, using click chemistry but without alkynylation or azidation of FCCs to be investigated. The proposed platform was systematically verified by biomimetic synthesis, liver microsomal incubation, and primary hepatocyte culture. A mixture of furan, 2-methylfuran, and 2,5-dimethylfuran as model was tested by use of the established platform. A total of hepatic 171 lysine-based adducted proteins and 145 cysteine-based adducted proteins by the reactive metabolites of the three FCCs were enriched and identified (Byonic score ≥ 100). The target proteins were found to mainly participate in ATP synthesis. The technique was also successfully applied to furan-containing natural products. The established platform made it possible to profile covalently adducted proteins, because of potential exposure to a vast inventory of over two million of FCCs documented.