The invention provides silicon-based composite film and a preparation method and application thereof; the silicon-based composite film comprises a silicon-based separator layer and a macromolecular film support layer connected with the silicon-based separator layer, wherein the silicon-based separator layer comprises, by weight, 50-150 parts of a silica polymer, 5-15 parts of a crosslinking agent, 0.1-1 part of a catalyst, and 100-3000 parts of a solvent. The macromolecular silica polymer is crosslinked to form the silicon-based separator layer, the silicon-based separator layer and the macromolecular film support layer are combined into the silicon-based composite film, Si in the macromolecular silica polymer forms stable chemical crosslinking structure so that the silicon-based composite film can exist stably in severe conditions, such as acids and bases or electrochemical condition; hydroxyl radicals at two side chain ends of the macromolecular silica polymer are separated from Si via methylene, and the stability of the chemical crosslinking structure is further ensured.