<p>Metal–organic frameworks typically rely on discrete molecules as building units, and creating frameworks featuring continuous organic or inorganic subnet moieties, such as chains and layers, is challenging. While all-inorganic subnets have been used as units with infinite connectivity, the intrinsic disorder in organic chains and layers hinders their role as well-defined building blocks for reticular materials. Here we report the one-pot synthesis of a series of Zr₆O₈-based or Hf₆O₈-based metal–organic frameworks that feature boroxine-based one-dimensional and two-dimensional covalent organic frameworks—chains with diverse conformations and layers with specific topology, respectively—as the organic components. The spatial compatibility between the constituents locks the infinite organic units into patterned arrangements and thus generates metal–organic frameworks with distinct structural entities and pore environments in separate sections along specific directions. The coexistence of extended covalent organic frameworks and discrete inorganic units, side by side and yet independent of each other, leads to high structural compartmentalization in space.</p><p></p>