For the more straightforward and more efficient solution of phononic crystal (PC) plate frequency band structure, transmission curve, and vibration mode, in this paper, related theories based on spatial Fourier series expansions, combined with Bloch’s theorem, a novel approach to solve the structural governing equations of PC plate is proposed by using the partial differential equations (PDE) module in the finite element software COMSOL. It is named the FE/PDE (Finite element and partial differential equations) method. The method’s accuracy is verified by comparing the results with those obtained from the traditional method. Systematic elucidation of the application of the method to probe the properties of multi-scale, multi-physics field coupled PC plate. In order to demonstrate the flexibility and scientific validity of the method, a novel nano-piezoelectric PC plate structure is proposed and solved. The method is simple, computationally efficient, and applicable, and provides a new method for investigating the properties of PC plates.