Two-dimensional (2D) covalent-organic frameworks (COFs) with a well-defined and tunable periodic porous skeleton are emerging candidates for lightweight and strong 2D polymeric materials. It remains challenging, however, to retain the superior mechanical properties of monolayer COFs in a multilayer stack. Here, we successfully demonstrated a precise layer control in synthesizing atomically thin COFs, enabling a systematic study of layer-dependent mechanical properties of 2D COFs with two different interlayer interactions. It was shown that the methoxy groups in COFTAPB-DMTP provided enhanced interlayer interactions, leading to layer-independent mechanical properties. In sharp contrast, mechanical properties of COFTAPB-PDA decreased significantly as the layer number increased. We attributed these results to higher energy barriers against interlayer sliding due to the presence of interlayer hydrogen bonds and possible mechanical interlocking in COFTAPB-DMTP, as revealed by density functional theory calculations.