Covalent organic frameworks (COFs) are prominent porous materials for molecules separation due to their desirable structures. However, very few COFs are reported for the separation of macromolecules such as low molecular-weight (MW) proteins. Here, two stable mesoporous COFs (Azo-COF and Tp-COF) with highly crystallized frameworks are synthesized, and their pore sizes are slightly-regulated via elaborate selection of pyrene knots and amino linkages. Benefiting from the pore size difference less than 4 Å, the tandem utilization of these two COFs exhibits efficiently size-selective separation ability towards low MW proteins cytochrome c and myoglobin with small MW difference of 2 kDa, in which protein adsorption possibilities are verified by computational calculations together with confocal laser scanning microscopy (CLSM). Furthermore, a simple COF-based separation device is designed and prepared to achieve effective and low-consumption proteins separation. This work has offered an optimized synthetic strategy for fine-tuned mesoporous COFs and expanded their applications on macromolecules separation.