Engineering the structure of materials endows them with novel physical properties across a wide range of length scales. With high in-plane stiffness and strength, but low flexural rigidity, two-dimensional (2D) materials are excellent building blocks for nanostructure engineering. They can be easily bent and folded to build three-dimensional (3D) architectures. Taking advantage of the large lattice mismatch between the constituents, we demonstrate a 3D heterogeneous architecture combining a basal Bi2Se3 nanoplate and wavelike Bi2Te3 edges buckling up and down forming periodic ripples. Unlike 2D heterostructures directly grown on substrates, the solution-based synthesis allows the heterostructures to be free from substrate influence during the formation process. The balance between bending and in-plane strain energies gives rise to controllable rippling of the material. Our experimental results show clear evidence that the wavelengths and amplitudes of the ripples are dependent on both the widths and thicknesses of the rippled material, matching well with continuum mechanics analysis. The rippled Bi2Se3/Bi2Te3 heterojunction broadens the horizon for the application of 2D materials heterojunction and the design and fabrication of 3D architectures based on them, which could provide a platform to enable nanoscale structure generation and associated photonic/electronic properties manipulation for optoelectronic and electromechanic applications.