Layered compounds characterized by van der Waals gaps are often associated with relatively weak interlayer particle interactions. However, in specific scenarios, these seemingly feeble forces can exert an impact on interlayer interactions through subtle energy fluctuations, which can give rise to a diverse range of physical and chemical properties, particularly intriguing in the context of thermal transport. In this study, taking a natural superlattice composed of alternately stacked PbS and SnS 2 sublayers as a model, we proposed that in a superlattice, there is strong hybridization between acoustic phonons of heavy sublayers and optical phonons of light sublayers. We identified newly generated vibration modes in the superlattice, such as interlayer shear and breathing, which exhibit lower sound velocity and contribute less to heat transport compared to their parent materials, which significantly alters the thermal behaviors of the superlattice compared to its bulk counterparts. Our findings on the behavior of interlayer phonons in superlattices not only can shed light on developing functional materials with enhanced thermal dissipation capabilities but also contribute to the broader field of condensed matter physics, offering insights into various fields, including thermoelectrics and phononic devices, and may pave the way for technological advancements in these areas.