Two-dimensional covalent organic frameworks (2D COFs) membranes have well-ordered nanochannels for selective molecular sieving. One-dimensional (1D) materials have been proposed to link the loosely packed COFs nanosheet for enhancing the separation performance of COFs membranes. However, it remains unclear how the enhancement arises. Herein, we demonstrate the role of 1D materials in modulating the microstructure and interlayer force of 2D COFs membranes. The optimized composite membrane, assembled from 2D COFs and chitosan exhibits a 75% enhancement in permeance without sacrificing selectivity towards different dyes. Our results show that the interaction forces between COFs and 1D materials are directly correlated to the transport nanochannels. When the interaction forces are stronger, the microstructure is more densely packed. Meanwhile, the shielding effect of 1D materials on the intrinsic channels of 2D COFs is more significant, resulting in narrow transport channels for mass transfer. In contrast, the weaker interaction forces prevent the excessive shrinkage of nanochannels, facilitating fast mass transfer and maintaining the high molecular selectivity. The work unravels the interaction forces between 2D COFs and 1D materials leading to the shaping of mass transfer nanochannels, offering a new perspective for the advancement of COFs membrane for nanofiltration.