In this work, two novel pyrimidine‐cored covalent organic frameworks TpTap‐COF and TpTan‐COF were synthesized for the first time and used for the adsorption of heavy metal ions in aqueous solution. Both COFs are nanofiber clusters with preferable crystallinity and thermal stability. The impact parameters such as pH value, shaking time, initial concentration, and temperature were studied by batch adsorption experiments in the multi‐metal ions system. The adsorption of six metal ions onto COFs follows the pseudo‐second‐order kinetic model and the Freundlich isotherm model, which is a chemical adsorption process that occurs on non‐uniform surfaces. The adsorption rate is determined by both film diffusion and intraparticle diffusion. Further research on the adsorption of copper ions onto COFs indicates the formation of metal complexes between O#N#N/O#O chelating sites in the COF skeleton and Cu ions through the sharing of lone pair electrons.