Photonic crystals are widely employed in industry fields due to their bandgap property, which can confine and propagate electromagnetic waves inside the structure as a photonic waveguide. As this property can be adopted to propagate distinct frequency waves by changing the photonic structure, photonic crystals are also applied in frequency demultiplexer design. The finite-difference time-domain (FDTD) method is commonly applied to simulate electromagnetic wave propagations in photonic crystals, helping determine the desired bandgaps for frequency demultiplexers. Meanwhile, the multivariate empirical mode decomposition (MEMD) nonlinearly decomposes multivariate signals in the instantaneous frequency domain. Therefore, MEMD can verify and visualize the designed frequency demultiplexer made of photonic crystals by considering simulation results as a multi-channel signal. This research aims to propose a method to design and evaluate frequency demultiplexers using FDTD and MEMD. In this paper, photonic crystal bandgaps are adopted to design a frequency demultiplexer to separate two different frequency electromagnetic waves. Then, MEMD is employed to the result of frequency demultiplexer propagation simulated by FDTD. Our results reveal that the frequency demultiplexer made of photonic crystals can be designed using the bandgap properties, and its simulation results by FDTD method can be verified and visualized in the instantaneous frequency domain using MEMD.