Organics separation for purifying and recycling environment-detrimental solvents is essential to sustainable chemical industries. Covalent organic framework (COF) membranes hold great promise in affording precise and fast organics separation. Nonetheless, how to well coordinate facile processing—high crystalline structure—high separation performance remains a critical issue and a grand challenging. Herein, we propose a concept of heterocrystalline membrane which comprises high-crystalline regions and low-crystalline regions. The heterocrystalline COF membranes are fabricated by a two-step procedure, i.e., dark reaction for the construction of high-crystalline regions followed by photo reaction for the construction of low-crystalline regions, thus linking the high-crystalline regions tightly and flexibly, blocking the defect in high-crystalline regions. Accordingly, the COF membrane exhibits sharp molecular sieving properties with unprecedented organic solvent permeance up to 44-times higher than the state-of-the-art membranes.