Covalent-organic frameworks (COFs) are regarded as promising candidates for many different energy/environmental applications, but these materials are more difficult to synthesize compared to other porous materials such as metal-organic frameworks (MOFs). Herein, we developed a computational screening algorithm that uses MOFs as substrates in order to theoretically allow heteroepitaxial growth of three-dimensional COFs (3D COFs). The algorithm details the interface of MOF@COF at the atomic/molecular level in order to create 3D COFs using a bottom-up approach. Consequently, 19 pairs of MOF@COF resulted from the algorithm are selected as candidates for heteroepitaxial growth of 3D COFs on the surface of MOFs.