The invention discloses a waterborne two-component quick-drying polymer cement waterproof mortar. The waterborne two-component quick-drying polymer cement waterproof mortar includes a powder materialand a liquid material, wherein the powder material is composed of the following components by mass percent: 35%-55% of Portland cement, 3%-12% of sulfur aluminum cement, 5%-25% of active filler, 25%-50% of ordinary filler, 0.2%-1.5% of anti-cracking fiber, and 0.1%-1.5% of an assistant; and the liquid material is composed of the following components by mass percent: 30%-50% of a polymer emulsion,0.1%-2% of an assistant, and the balance water; and the powder material and liquid material are mixed in a ratio of 2.5-4:1. Compared with the prior art, the invention realizes one-time thick coatingof polymer cement waterproof mortar, which can dry quickly, does not crack, and has good impermeability. The construction and maintenance time can be shortened to 4h, and the construction period is greatly shortened. The waterborne two-component quick-drying polymer cement waterproof mortar provided by the invention has the characteristics of high bonding strength, good resistance to water and alkali, and good weatherability, can be directly applied to construction on base planes without open water, and can be widely applied to basement, kitchen, toilet, bathroom, swimming pool, balcony, garden waterscape, interior and exterior wall integral waterproofing and seepage prevention, and other waterproofing projects.