The invention discloses a lithium ion battery composite diaphragm and a preparation method and an application thereof, belonging to the technical field of lithium ion batteries. The composite diaphragm comprises a polyolefin microporous membrane, a polymer microsphere based coating on one side surface of the polyolefin microporous membrane, and an inorganic ceramic-based coating on the other side surface of the polyolefin microporous membrane. The lithium ion battery composite diaphragm has good air permeability, liquid retaining capability and high-temperature resistance and can remarkably improve the security and the circulation property of the battery. The melting point or softening point of the polymer microsphere-based coating in the composite diaphragm is 90-140 DEG C, and when the temperature of the battery is increased, the polymer microsphere based coating is molten or swelled within a short time, then the apertures of the polyolefin microporous membrane are blocked rapidly, the thermal turn-off effect of the diaphragm is achieved, a lithium ion conveying channel is cut off, and short circuit inside the battery is prevented; meanwhile as ceramic grains inside the inorganic ceramic-based coating have the high-temperature resistance property, the polyolefin microporous membrane is effectively prevented from shrinkage, and the situation that positive and negative films directly come into contact to cause short circuit of the battery.