We present a direct observation of a structural transition at molecular scale in an organic p-nitrobenzonitrile (PNBN) thin film using scanning tunneling microscopy (STM). STM images clearly show an ordered molecular structure of unrecorded regions in the films, while the PNBN molecular arrangements are disordered in the recorded regions. The current-voltage (I-V) measurements from the STM demonstrate a great increase of the conductance transition in the recorded regions after the voltage pulses. Those results suggest that the recording mechanism may be due to a crystalline structural transition, which is consistent with our previously proposed mechanism in another organic system for ultrahigh density data storage.