Boron affinity molecular imprinting technology has the advantages of high imprinting efficiency, strong affinity, and the combination and release of pH regulation because of the reversible covalent binding of boric acid ligands to cis-dihydroxy compounds, and it is widely used in separation and enrichment of cis-diol complexes base molecule. We introduced the application of boron affinity molecular imprinting technology in the identification and enrichment of nucleotides, sugars, glycoproteins, cells and bacteria, and prospected for the future development of this technology.