The central feature of covalent organic frameworks (COFs) is crystallinity which is conducive to forming a uniform pore structure. However, synthesis of highly crystalline COFs based on stable covalent bonds remains formidable task. In this paper, a highly crystalline acylhydrazone COF-BD was synthesized in aqueous phase. The synthesis mechanism was proposed that the protonated hydrazide monomers dissolved in aqueous phase reacted with aldehyde monomers by deprotonation into the micellar. By investigating the effects of experimental parameters on the crystallinity of COF-BD, it was founded that under C9–COONa as surfactant, 80 °C, and 1.0 eq acetic acid as catalyst, acylhydrazone COF-BD with good crystallinity could be prepared. To prove the extensibility of this method, another acylhydrazone COF was prepared successfully.