The invention provides a meso-structural chitosan-phosphotungstic acid proton exchange membrane and a preparation method thereof. The preparation method comprises the following steps: step A, preparing an acetic acid solution of chitosan; step B, preparing a tri-block copolymer P123 solution; step C, mixing the chitosan solution and the P123 solution, stirring, and then casting to prepare membranes; step D, carrying out a post treatment on the prepared membranes to remove the acetic acid and P123 so as to obtain the mesoporous chitosan membranes; step E, dipping the membranes obtained in the step D into a phosphotungstic acid solution so as to obtain the meso-structural chitosan-phosphotungstic acid proton exchange membrane. The prepared proton exchange membrane has the advantages of high electrical conductivity and low methanol penetration coefficient, and is suitable for being directly applied to methanol fuel cells as a proton exchange membrane. At the same time, the preparation method has the advantages of wide raw material sources and low prices.