Recent efforts in growing two-dimensional (2D) multilayers have enabled the synthesis of single crystalline 2D multilayers in a wafer scale through the seamless stitching of multiple epitaxial 2D islands. Unlike previously observed wedding-cake or inverted-wedding-cake structures, these multilayer islands have the same size and shape in each layer with aligned edges. In this study, we investigated the underlying growth mechanisms of synchronic 2D multilayers growth and have showed that a heterogenous layer on a crystalline substrate is critical for maintaining the synchronic growth of 2D multilayers. During growth, the heterogenous layer passivates the edges of multilayer 2D island and thus prevents the coalescence of these active edges, while the high interfacial energy between the heterogenous surface layer and the substrate stabilizes the synchronic structure. Based on this model, we have successfully explained the previously observed synchronic growth of graphene and hexagonal boron nitride multilayers (Nat Nanotech 2020, 15: 861; Nature 2022, 606: 88). The deep understanding on the mechanism paves a way towards the synthesis of wafer-scale single-crystal 2D multilayers with a uniform thickness.