Two-dimensional covalent organic frameworks (2D COFs) featuring periodic frameworks, extended π-conjugation and layered stacking structures, have emerged as a promising class of materials for photocatalytic hydrogen evolution. Nevertheless, the layer-by-layer assembly in 2D COFs is not stable during the photocatalytic cycling in water, causing disordered stacking and declined activity. Here, we report an innovative strategy to stabilize the ordered arrangement of layered structures in 2D COFs for hydrogen evolution. Polyethylene glycol is filled up in the mesopore channels of a β-ketoenamine-linked COF containing benzothiadiazole moiety. This unique feature suppresses the dislocation of neighbouring layers and retains the columnar π-orbital arrays to facilitate free charge transport. The hydrogen evolution rate is therefore remarkably promoted under visible irradiation compared with that of the pristine COF. This study provides a general post-functionalization strategy for 2D COFs to enhance photocatalytic performances.