The invention provides a polyene microporous multilayer diaphragm and a manufacturing method thereof. The diaphragm is formed by combing three or more than three polyene layers, wherein in a plurality of polyene layers, at least one polyene layer is a polyethylene layer, and at least one polyene layer is a polypropylene layer; the polyethylene layer and the polypropylene layer are tightly attached to each other; and in adjacent polyethylene and polypropylene layers, at least one layer is a polymer blend layer which contains a certain amount of ethylene-propylene copolymer. The invention has the advantages that: in the integrated structure of the polyene microporous multilayer diaphragm, the properties of porosity, puncture strength, pore size, ventilation ratio, tensile strength, breaking elongation and the like are also identical to the high properties of a single-layer diaphragm; simultaneously, the defects of the single-layer diaphragm is overcome, namely the safety of the diaphragm is improved.