Designing the 3D structure of 2D nanomaterials is one of the effective measures to enhance their wear resistant. Here, we used graphene oxide (GO) as a template and selected mono-aminopropyllsobutyl polyhedral oligomeric silsesquioxane (MAPOSS) and octa-aminophenyl polyhedral oligomeric silsesquioxane (OAPOSS) to prepare a “plate-anchor” shaped MAPOSS-GO (2D) and three-dimensional cross-linked “soft ladder” shaped OAPOSS-GO (3D). From the friction experiments (0.5 N), the lubricant film formed by OAPOSS-GO (393 nm) is thicker and more regular than MAPOSS-GO (268 nm) and GO (70 nm). The wear life of OAPOSS-GO (289 min) is higher than that of MAPOSS-GO (174 min) and GO (49 min). Molecular dynamics simulations (MD) further revealed the reasons for the improved wear resistance of the OAPOSS-GO. Firstly, Polyhedral Oligomeric Silsesquioxane (POSS) improves GO-substrate binding and promotes a more regular arrangement of nanosheets. Secondly, the covalent bond between OAPOSS and GO resists the friction of the nanosheets during the sliding process, resulting in the formation of a thicker lubrication film; thirdly, the “soft ladder” structure facilitates the formation of physical occlusion without covalent bonding between different nanosheets, increasing the stability of the lubrication film. Therefore, our study provides a theoretical basis for the preparation of highly wear-resistant layered nanomaterials.