The invention relates to a method for preparing an organic-inorganic multilayer composite proton exchange membrane by an in-situ mineralization method, wherein a polymer matrix can be prepared into asmooth or porous matrix membrane by casting or phase separation method, and then a polydopamine (PDA) coating is deposited on the membrane surface by a room temperature air oxidation method; Finally,the matrix films of polydopamine are deposited in Zr (SO4) 2 solution and mineralized in situ. ZrO2- PDA with sandwich structure is prepared by adjusting the deposition time, temperature and pH valueto modify the Organic--Inorganic composite proton exchange membrane. The composite proton exchange membrane prepared by the invention has the characteristics of high high-temperature water retention rate, high proton conductivity and low swelling rate when the temperature is above 80 DEG C, and the preparation method has low energy consumption, high efficiency and is easy to be produced on a largescale.