Since molecular electronics has been rapidly growing as a promising alternative to conventional electronics towards the ultimate miniaturization of electronic devices through the bottom-up strategy, it has become a long-term desire to understand and control the transport properties at the level of single molecules. In this Research News article it is shown that one may modify the electronic states of single molecules and thus control their transport properties through designing and fabrication of functional molecules or manipulating molecules with scanning tunneling microscopy. The rectifying effect of single molecules can be realized by designing a donor–barrier–acceptor architecture of Pyridine–σ–C60 molecules to achieve the Aviram–Ratner rectifier and by modifying electronic states through azafullerene C59N molecules. The effect of the negative differential resistances can be realized by appropriately matching the molecular orbital symmetries between a cobalt phthalocyanine (CoPc) molecule and a Ni electrode. The electronic states and transport properties of single molecules, such as CoPc and melamine molecules, can be altered through manipulation or modifying molecular structures, leading to functionalized molecular devices.