CD44 is the principle cell surface receptor for the extracellular matrix. The altered expression or dysfunction of CD44 proteins contributes to numerous pathological processes. Therefore, it is very necessary to detect the distribution and density of CD44 proteins on cell surface. In this paper, the unbinding force between the tip of an atomic force microscope modified with anti-human CD44 antibody (a kind of CD44 pathway ligation proteins, currently used to induce the apoptosis of some types of tumors) and B16 (human melanoma cell line) cells was measured. The results indicated that the distribution of CD44 was nonuniform and represented clusters on B16 cell surface. And, the data of kinetics of CD44 antibody-antigen binding experiments indicated that the CD44 signal pathway in B16 cells could be blocked by anti-CD44 monoclonal antibody. This methodology can be extended to the evaluation and screening of molecular targeted drugs for pharmacological use.