Abstract: This study investigates if the vibration frequency and amplitude, coupled with cutting parameters could reduce the thrust force in the drilling of CFRP/Al stacks. In the ANOVA and main-effect plots, the contributions (PCRs) of the vibrating amplitude were high (CFRP: 80.14%, Al: 48.14%). When drilling in the steady states, the interactions between the employed vibration parameters with the machine tool and the fixation system were interpreted using the empirical mode decomposition (EMD) and Fourier spectrum with appreciable results (CFRP: R2 = 84.1%, Al: R2 = 93.9%). When drilling in the CFRP layer at the cutting onsets, the resolved spectrums perfectly matched the mechanical effects in the cutting stage (19.5–1367 Hz), with chattered-induced vibration (683.6 and 1367 Hz). When drilling of the Al layer, the damping-induced vibration led to an increase in the background noises (39.1–117.2 Hz), whereas the frequencies produced by the spindle remained largely the same.