We propose the multi-layered cepstrum (MLC) method to estimate multiple fundamental frequencies (MF0) of a signal under challenging contamination such as high-pass filter noise. Taking the operation of cepstrum (i.e., Fourier transform, filtering, and nonlinear activation) recursively, MLC is shown as an efficient method to enhance MF0 saliency in a step-by-step manner. Evaluation on a real-world polyphonic music dataset under both normal and low-fidelity conditions demonstrates the potential of MLC.