Crystalline solids typically show robust long-range structural ordering, vital for their remarkable electronic properties and use in functional electronics, albeit with limited customization space. By contrast, synthetic molecular systems provide highly tunable structural topologies and versatile functionalities but are often too delicate for scalable electronic integration. Combining these two systems could harness the strengths of both, yet realizing this integration is challenging owing to distinct chemical bonding structures and processing conditions. Two-dimensional atomic crystals comprise crystalline atomic layers separated by non-bonding van der Waals gaps, allowing diverse atomic or molecular intercalants to be inserted without disrupting existing covalent bonds. This enables the creation of a diverse set of layered hybrid superlattices (LHSLs) composed of alternating crystalline atomic layers of variable electronic properties and self-assembled atomic or molecular interlayers featuring customizable chemical compositions and structural motifs. Here we outline strategies to prepare LHSLs and discuss emergent properties. With the versatile molecular design strategies and modular assembly processes, LHSLs offer vast flexibility for weaving distinct chemical constituents and quantum properties into monolithic artificial solids with a designable three-dimensional potential landscape. This opens unprecedented opportunities to tailor charge correlations, quantum properties and topological phases, thereby defining a rich material platform for advancing quantum information science.