We demonstrate optimization of thermal conductance across nanostructures by developing a method combining atomistic Green's function and Bayesian optimization.With an aim to minimize and maximize the interfacial thermal conductance (ITC) across Si-Si and Si-Ge interfaces by means of Si/Ge composite interfacial structure, the method identifies the optimal structures from calculations of only a few percent of the entire candidates (over 60,000 structures). The obtained optimal interfacial structures are non-intuitive and impacting: the minimum-ITC structure is an aperiodic superlattice 2 that realizes 50% reduction from the best periodic superlattice. The physical mechanism of the minimum ITC can be understood in terms of crossover of the two effects on phonon transport: as the layer thickness in superlattice increases, the impact of Fabry-Pérot interference increases, and the rate of reflection at the layer-interfaces decreases.Aperiodic superlattice with spatial variation in the layer thickness has a degree of freedom to realize optimal balance between the above two competing mechanism.Furthermore, aperiodicity breaks the constructive phonon interference between the interfaces inhibiting the coherent phonon transport. The present work shows the effectiveness and advantage of material informatics in designing nanostructures to control heat conduction, which can be extended to other interfacial structures.