Abstract: Single molecule science is a new emerging cross discipline, and is significant in current development of the sciences and technologies. Scanning tunneling microscope (STM) is a powerful and unique technique to research the single molecule. In this review, we will summarize application of STM in single molecular science, with some recent progresses on characterizing, manipulation single molecule and designing related molecular device by our group being introduced as typical examples as follows: the native cage structure of C60 molecule on self -assembled monolayer of alkylthiol was observed, and a new topological order originating from the orientation of C60 molecule was found; by combining the experimental images and theoretical simulations, the orientation of C60molecule on Si(111)-7×7surface was identified; the energy-resolved metal-cage hybrid states of single Dy@C82 molecule were mapped, and then the relative position of the metal atom inside the cage and the molecular orientation was inferred by comparing the experimental results and the theoretical simulations; by performing “molecular operation” to the CoPc molecule on Au(111) surface by using STM tip, the adsorption state and spin state of the CoPc molecule was controlled; based on single electron tunneling effect and special energy structure of C59N molecule, a new mechanism of molecular rectifying was built; a negative differential resistance effect related to local orbital symmetry matching between the Co atom in single CoPc molecule and STM tip was found.