This paper systematically compares the numerical implementation and computational cost between the Fourier spectral iterative perturbation method (FSIPM) and the finite element method (FEM) in solving partial differential equilibrium equations with inhomogeneous material coefficients and eigenfields (e.g., stress-free strain and spontaneous electric polarization) involved in phase-field models. Four benchmark numerical examples, including inhomogeneous elastic, electrostatic, and steady-state heat conduction problems demonstrate that (1) the FSIPM rigorously requires uniform hexahedral (3D) and quadrilateral (2D) mesh and periodic boundary conditions for numerical implementation while the FEM permits arbitrary mesh and boundary conditions; (2) the FSIPM solutions are comparable to their FEM counterparts, and both of them agree with the analytic solutions, (3) the FSIPM is much faster in solving equilibrium equations than the FEM to achieve the accurate solutions, thus exhibiting a greater potential for large-scale 3D computations.