We observed the surface resistance of copper(II) phthalocyanine (Cu-Pc) thin films dependence on substrate heat-treatment conditions by a nondestructive characterization method using a near-field scanning microwave microscope (NSMM) at an operating frequency f=5.2–5.3 GHz. The changes in surface resistance were investigated by NSMM by measuring the reflection coefficient S 11. The surface resistance of Cu-Pc thin films depends on the grain alignment. When the Cu-Pc thin films were annealed at 150 °C for 3 h, the films are aligned with the b-axis normal to the substrate and have a lower surface resistance.