Van der Waals heterostructures have great potential for realizing ultimately low thermal conductivity because defectless interfaces can be constructed at a length scale smaller than the phonon wavelength, allowing modulation of coherent phonon transport. In this Letter, we demonstrate the mechanism for thermal conductivity reduction at a mode-resolved level. The graphene-WS2 heterostructure with the lowest cross-plane thermal conductivity of 0.048 W/(m·K) is identified from 16,384 candidates by combining Bayesian optimization and molecular dynamics simulations. Then, the angle-resolved phonon transmission is calculated using the mode-resolved atomistic Green's function. The results reveal that the optimal heterostructure nearly completely terminates phonon transport with finite incident angles, owing to the reduced critical incident angle and suppression of phonon tunneling.