The phonon thermal conductivity of misfit-layered Ca3Co4O9 has been calculated by perturbed molecular dynamics using a classical force field. Detailed numerical analyses reveal that, in spite of its smaller cross-sectional area, the CoO2 layer transports more heat than the thicker rock salt (RS) layer, although its local thermal conduction is more suppressed than in another layered cobaltite, Na x CoO2. The origins of these differences have been elucidated through careful examination of the atomic arrangements in each layer. Since thermal conduction in the RS layer can be reduced without deteriorating electronic properties for which the CoO2 layer is responsible, it is suggested that the RS layer should be modified to further suppress the overall in-plane thermal conductivity. Computational experiments with increasing number of Ca–O planes in the RS layer showed the opposite trend to what can be predicted based on the misfit between two dissimilar layers. Further analyses to reveal the origin of these unexpected results provide yet another strategy to further decrease the thermal conductivity, namely to control the dynamic interference between atoms across the interface between two layers.