Research on two-dimensional (2D) materials and related van der Waals heterostructures (vdWHs) is intense and remains one of the leading topics in condensed matter physics. Lattice vibrations or phonons of a vdWH provide rich information, such as lattice structure, phonon dispersion, electronic band structure and electron–phonon coupling. Here, we provide a mini review on the lattice vibrations in vdWHs probed by Raman spectroscopy. First, we introduced different kinds of vdWHs, including their structures, properties and potential applications. Second, we discussed interlayer and intralayer phonon in twist multilayer graphene and MoS₂. The frequencies of interlayer and intralayer modes can be reproduced by linear chain model (LCM) and phonon folding induced by periodical moiré potentials, respectively. Then, we extended LCM to vdWHs formed by distinct 2D materials, such as MoS₂/graphene and hBN/WS₂ heterostructures. We further demonstrated how to calculate Raman intensity of interlayer modes in vdWHs by interlayer polarizability model.