We report the changes of the microwave reflection coefficients S$_{11}$ of copper(II)-phthalocyanine (CuPc) thin films by using a near-field microwave microscope(NSMM) in order to understand the phase transition of CuPc. For a NSMM system, a high-quality microstrip resonator coupled with a dielectric resonator was used. CuPc thin films were prepared on the pre-heated glass substrates using a thermal evaporation method. The reflection coefficients S$_{11}$ of CuPc thin films were changed by the dependence on the substrate pre-heating temperatures. By comparing reflection coefficient S$_{11}$ and crystal structures, we found the phase transition of CuPc thin films from $alpha$-phase to $eta$-phase at the substrate heating temperature 200 $^{circ}C$./TEX>.