We have studied the effect of metal ions on the specific interaction between a protein, immunoglobulin E (IgE), and its 37-nt DNA aptamer with atomic force microscopy (AFM). Protein aptamers are a new class of synthetic single-stranded DNA/RNA oligonucleotide generated from in vitro selection to selectively bind with target proteins. The IgE aptamers have been developed and are expected to be promising reagents in IgE detection and new anti-allergic drug development. It is known that the presence of metal ions in the buffer usually has a strong effect on the affinity of single-stranded DNA for protein. In this work, the effect of two representative monovalent ion and divalent ion on the binding of IgE and the aptamer has been studied at the single-molecule level. The results from the AFM force measurements show that the metal ions not only reduce the single-molecular rupture force but also reduce the number of bonds formed between IgE and the aptamer.