Superexchange coupling in poly-p-phenylene molecular wires was probed using scanning tunneling microscopy/spectroscopy at cryogenic temperatures. The coupling strength was characterized by measuring the energy splitting between the molecular states constructed by symmetric and antisynnmetric dimerization of molecular fragments' orbitals. The results confirm the theoretically predicted exponential decay behavior of the superexchange coupling on a single-molecule level. A decay constant of 0.10 +/- 0.02 angstrom(-1), was obtained. Owing to the high spatial resolution of scanning tunneling microscopy, the molecules' internal states (e.g., molecular conformation) as well as external states (e.g., interaction with foreign atoms or molecules) were elucidated with atomic precision at the mean time of characterizing the superexchange coupling. This method provides a new approach to quantify how intramolecular charge transfer is influenced by molecular conformation and interaction with the surroundings.