The invention relates to a complex water-based polymer waterproof coating and a manufacturing method thereof. The manufacturing materials comprise the following components in parts by weight: A, organic liquid and B, inorganic fillers, wherein the organic liquid consists of 500-1000 parts of water-based latex, 100-150 parts of water-borne epoxy resin, 5-10 parts of wetting dispersant and 5-10 parts of antifoaming agent; and the inorganic fillers consist of 250-500 parts of inorganic low-cementitious material, 50-100 parts of silica fume, 100-300 parts of calcium carbonate, 100-250 parts of quartz powder, 50-100 parts of talcum powder and 50-100 parts of bentonite. The complex water-based polymer waterproof coating disclosed by the invention has the characteristics of good waterproof performance, durable weather resistance, stable performance, high temperature resistance, freeze thawing resistance, simplicity and convenience in construction, wide application range, utilization of industrial solid wastes and the like. In addition, the product is compounded into a pasty flowing slurry and is directly used on site, the cost is saved, and the defects such as dust pollution are avoided.