5-Hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) are key intermediates of active DNA demethylation, for which the global detection methods are still restricted by high cost and long operation time. Here, we demonstrate a pearl necklacelike strategy to accurately quantify global 5hmC and 5fC in genomic DNA. In this method, the metal-organic framework (MOF), [Cu3(BTC)2] (denoted as HKUST-1, H3BTC = 1,3,5-benzenetricarboxylic acid), with a diameter of ∼30 nm that contains ∼15 000 copper ions (Cu2+) as the "super label" was in situ grown in the carboxylated 5hmC and 5fC loci of genomic DNA via the coordination between Cu2+ and the carboxyl group. After the acid digestion of MOF, the concentration of Cu2+, which has a quantitative relationship with the 5hmC/5fC content, was measured by inductively coupled plasma-atomic emission spectroscopy (ICP-AES). The metal element enrichment during MOF growth has amplified the signal by 4 orders of magnitude, realizing sensitive and accurate quantification of global 5hmC and 5fC in different tissues with a detection limit of 0.031% and 0.019‰ in DNA, respectively. The bisulfite- and mass spectrometry-free strategy is easily performed in almost all research and medical laboratories and would provide potential capability to quantify other candidate modifications in nucleotides.