We report an inelastic neutron scattering study on the spin resonance in the bilayer iron-based superconductor CaKFe$_4$As$_4$. In contrast to its quasi-two-dimensional electron structure, three strongly $L$-dependent modes of spin resonance are found below $T_c=35$ K. The mode energies are below and linearly scale with the total superconducting gaps summed on the nesting hole and electron pockets, essentially in agreement with the results in cuprate and heavy fermion superconductors. This observation supports the sign-reversed Cooper pairing mechanism under multiple pairing channels and resolves the long-standing puzzles concerning the broadening and dispersive spin resonance peak in iron pnictides. More importantly, the triple resonant modes can be classified into odd and even symmetries with respect to the distance of Fe-Fe planes within the Fe-As bilayer unit. Thus, our results closely resemble those in the bilayer cuprates with nondegenerate spin excitations, suggesting that these two high-$T_c$ superconducting families share a common nature.