A real-time method to observe both the structural and the electronic configuration of an organic molecule during deposition is reported for the model system of pentacene on graphite. Structural phase transition of the thin films as a function of coverage is monitored by using in situ angle resolved photoemission spectroscopy (ARPES) results to observe the change of the electronic configuration at the same time. A photoemission theory that uses independent atomic center approximations is introduced to identify the molecular orientation from the ARPES technique. This study provides a practical insight into interpreting ARPES data regarding dynamic changes of molecular orientation during initial growth of molecules on a well-defined surface.