Silicon (Si) is a promising anode material to realize many-fold higher anode capacity in next-generation lithium-ion batteries (LIBs). Si electrochemistry has strong dependence on the property of the Si interface, and therefore, Si surface engineering has attracted considerable research interest to address the challenges of Si electrodes such as dramatic volume changes and the high reactivity of Si surface. Molecular nanostructures, including metal–organic frameworks (MOFs), covalent–organic frameworks (COFs) and monolayers, have been employed in recent years to decorate or functionalize Si anode surfaces to improve their electrochemical performance. These materials have the advantages of facile preparation, nanoscale controllability and structural diversity, and thus could be utilized as versatile platforms for Si surface modification. This review aims to summarize the recent applications of MOFs, COFs and monolayers for Si anode development. The functionalities and common design strategies of these molecular structures are demonstrated.