A molecular-level photodiode was fabricated using a phase separation technique. The separated phase of a stacked layer of flavin (sensitizer (S))-ODTCS (octadecyl trichlorosilane) mixture and PFCA (nonadecafluoro-decanoic acid) was constructed and observed by AFM. Based on this structure, a submicron scale electron donor (D)/S/relay (R)/acceptor (A) molecular photodiode was fabricated on the silicon wafer substrate by the LB method. The morphology of the device was confirmed by AFM. The photodiode effect of the molecular device was observed using STM. The molecular scale photodiode and photoswitching effect could be verified.