The invention provides a composite waterproofing layer and a preparation and construction method thereof. The method comprises the steps that polymer waterproofing mortar is sprayed on a concrete primary lining to form a polymer waterproofing mortar layer which adheres to the concrete primary lining; an asphalt waterproofing coating is sprayed on the polymer waterproofing mortar layer to form an asphalt waterproofing coating layer which adheres to the polymer waterproofing mortar layer to obtain a composite waterproofing layer, wherein the asphalt waterproofing coating is formed by negative ion emulsified asphalt modified by vulcanized rubber, rubber emulsion, additive and filler, and the filler comprises at least one of fumed silica and barium sulfate; reinforcing bars are fastened on thecomposite waterproofing layer, and a concrete secondary lining is formed by concrete pouring. The concrete primary lining, the polymer waterproofing mortar layer, the asphalt waterproofing coating layer and the concrete secondary lining can firmly adhere to each other, the composite waterproofing layer has the advantages of stable structure and the like, undesirable phenomena of water leakage andthe like are reduced, and therefore the quality of a waterproofing project is improved.