We have investigated the conductivity variation of copper phthalocyanine nano-crystals deposited on SiO2 and mica. The density of surface hydroxyl group on SiO2 was estimated to be more than 10 times larger than that on mica by X-ray photoelectron spectroscopy. The grown crystals on both substrates were categorized to be a-axis orientation of α–form. Conductance-distance (G-d) measurements for various crystalline grains having different heights have been carried out with current imaging using atomic force microscope. The obtained conductivity vs. crystal height plot indicates that lower height crystals have higher conductivities on both surfaces. Besides, the lower height crystals on SiO2 have higher conductivity than those on mica. These results suggest that the electrons in the bottommost molecular layer are transferred to the electrophilic functional groups on the substrate surface. Such a phenomenon at organic semiconductor/insulator interface is reported for the first time.