The present invention relates to a process for preparing a metal ion imprinted polymer which can selectively separate heavy metal ions, comprising: (a) reacting a metal salt and a monomer to make a monomer containing a metal ion group; (b) mixing the monomer containing the metal ion group, a cross-linker and an initiator in a solvent; (c) suspension polymerizing or emulsion polymerizing the obtained mixture to obtain a metal ion imprinted polymer containing a metal ion; and (d) removing the imprinted metal ion from said metal ion imprinted polymer.