The effects of the electric-field-assisted annealing on the bulk heterojunction nanomorphology in the P3HT/PCBM active layer of the organic photovoltaic cells (OPVCs) are presented here. It was widely accepted that the electric-field-assisted annealing will facilitate the P3HT, the polar polymer, to be better crystalline to enhance the charge mobility, hence the improvement of the OPVC performance. The influences on the nano-morphology of the electron donor and accepter domains are not well understood. Here, using the cross-sectional scanning tunneling microscopy and spectroscopy (XSTM/S), the electric-field-assisted annealing treatment is found to influence the molecular domains to be elongated with the orientation near the direction of the external electric field. The elongation of the molecular domains is believed to facilitate the domain percolation, which causes higher charge mobility, hence the higher short-circuit current density (Jsc). On the other hand, it was also observed that the electronic properties of the P3HTrich and PCBM-rich domains in the electric-field-assisted annealed samples showed smaller