The generator coordinate method of a microscopic cluster model is developed to treat the resonance and scattering of nuclear clusters with complex scaling. We consistently derive the formulation of the complex scaling for the microscopic cluster model, in which only the relative motions between clusters are transformed in the generator coordinate wave function. We also reveal the applicability of this method to the cluster wave function. Furthermore, we demonstrate this framework in the 2$\alpha$ system of $^8$Be and obtain the solutions of resonance and non-resonant continuum states. Using these solutions, we calculate the level density, which brings the phase shifts of the cluster-cluster scattering. This work becomes the foundation in the description of the multi-cluster scattering states of nuclei in a microscopic framework with complex scaling.