Belonging to the technical field of lithium ion batteries, the invention discloses a lithium ion battery composite diaphragm and a preparation method thereof. The composite diaphragm comprises a polyolefin diaphragm and a fluorine-containing macromolecular polymer coating covering at least one surface of the polyolefin diaphragm. Compared with existing polyolefin diaphragms, the composite diaphragm has significantly enhanced thermal stability and safety, and plays a flame retardant role. At the same time, according to the invention, a composite surfactant, a composite silicone defoaming agent, an emulsion suspension stabilizer and a polyether silicone oil leveling agent are added into a polyacrylate cladded fluorine-containing emulsion to perform modification, and the coating performance of the fluorine-containing macromolecular polymer emulsion is improved. The preparation method for the composite diaphragm provided by the invention is simple, and is suitable for large-scale industrial production and application.