Crystalline porous materials such as covalent organic frameworks (COFs) are advanced materials to tackle challenges of catalysis and separation in industrial processes. Their synthetic routes often require elevated temperatures, closed systems with high pressure, and long reaction times, hampering their industrial applications. Here we use a traditionally unperceived strategy to assemble highly crystalline COFs by electron beam irradiation with controlled received dosage, contrasting sharply with the previous observation that radiation damages the crystallinity of solids. Such synthesis by electron beam irradiation can be achieved under ambient conditions within minutes, and the process is amendable for large-scale production. The intense and targeted energy input to the reactants leads to new reaction pathways that favor COF formation in nearly quantitative yield. This strategy is applicable not only to known COFs but also to new series of flexible COFs that are difficult to obtain using traditional methods.