It has been a longstanding challenge to rationally synthesize thin films of organic two-dimensional (2D) crystals with large single-crystalline domains. Here, we present a general strategy for the creation of 2D crystals of covalent organic frameworks (COFs) on the water surface, assisted by a charged polymer. The morphology of the preorganized monomers underneath the charged polymer on the water surface and their diffusion were crucial for the formation of the organic 2D crystals. Thin films of 2D COFs with an average single-crystalline domain size of around 3.57 ± 2.57 μm2 have been achieved, and their lattice structure, molecular structure, and grain boundaries were identified with a resolution down to 3 Å. The swing of chain segments and lattice distortion were revealed as key factors in compensating for the misorientation between adjacent grains and facilitating error corrections at the grain boundaries, giving rise to larger single-crystalline domains. The generality of the synthesis method was further proved with three additional 2D COFs. The oriented single-crystalline domains and clear grain boundaries render the films as model materials to study the dependence of the vertical conductivity of organic 2D crystals on domain sizes and chemical structures, and significant grain boundary effects were illustrated. This study presents a breakthrough in the controlled synthesis of organic 2D crystals with structural control at the molecular level. We envisage that this work will inspire further investigation into the microstructure-intrinsic property correlation of 2D COFs and boost their application in electronics.