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Despite rapid progress in recent years, it has remained challenging to prepare crystalline two-dimensional polymers. Here, we report the controlled synthesis of few-layer two-dimensional polyimide crystals on the surface of water through reaction between amine and anhydride monomers, assisted by surfactant monolayers. We obtained polymers with high crystallinity, thickness of ~2 nm and an average crystal domain size of ~3.5 μm2. The molecular structure of the materials, their grain boundaries and their edge structures were characterized using X-ray scattering and transmission electron microscopy techniques. These characterizations were supported by computations. The formation of crystalline polymers is attributed to the pre-organization of monomers at the water–surfactant interface. The surfactant, depending on its polar head, promoted the arrangement of the monomers—and in turn their polymerization—either horizontally or vertically with respect to the water surface. The latter was observed with a surfactant bearing a carboxylic acid group, which anchored amine monomers vertically through a condensation reaction. In both instances, micrometre-sized, few-layer two-dimensional polyamide crystals were grown. It is difficult to prepare 2D polymers that are crystalline over large areas. Now, few-layer 2D polyimides and polyamides with good crystallinity on the micrometre scale have been synthesized on a water surface. A surfactant monolayer is used to organize amine monomers before their polymerization with anhydride moieties.