Two-dimensional (2D) materials are promising in reducing friction-induced energy loss and wear in automotive and electronics industries because of their superior tribological performance. As a kind of organic 2D materials, the structure and functionality of covalent organic frameworks (COFs) are much easier to tailor compared to other inorganic 2D materials, which expand their potential application in a Micro-Electro-Mechanical System (MEMS). In this manuscript, several kinds of COFs are synthesized and characterized on the surface of highly oriented pyrolytic graphite (HOPG) to investigate the nanotribological mechanism of organic 2D materials. It is surprisingly revealed that the friction coefficients of surface COFs are positively correlated with the pore sizes of honeycomb networks. The COFs with smaller pores would have a smoother potential energy surface and exhibit a lower friction coefficient. Besides, the porous structures of surface COFs make them good candidates to be host templates. The host-guest assembly structures are successfully constructed after introducing coronene molecules, and these host-guest systems display higher friction coefficients because the assembly structure of the guest molecules would be perturbed during the friction process and bring additional slip energy barriers, but the capacity of COFs to form composite assembly with functional guest molecules greatly promotes their further application in the MEMS.