The vast structural diversity of metal–organic frameworks (MOFs) and the ability to tailor the structures makes the materials applicable for a broad range of uses. Traditional bottom-up and top-down design approaches have enabled a rapid increase in this structural diversity, yet the systematic screening for unknown synthesizable MOFs remains a challenge. Here we report a design strategy, the up–down approach, by merging the bottom-up and top-down approaches. This approach bridges the advantages of both methods, creating a synergistic strategy for discovering MOF structures. Targeting Zr-based MOFs, we search promising topology candidates and unveiled 26 future structural configurations by considering the possible orientations of Zr6 clusters. Through ribbon representation and sophisticated analysis of the ligand angles, we suggest structure models and synthesize Zr6-based MOFs with bct (1) and scu (1) configurations. The up–down approach will accelerate the discovery of previously unknown or inaccessible MOFs, providing exciting opportunities to expand the chemical space of MOFs.