The invention discloses an environment-friendly building waterproof paint with a low content of VOC (volatile organic compound) and a preparation method thereof. The paint comprises the following components in parts by weight: 3 to 6.5 parts of water, 0.01 to 0.05 part of thickening agent, 0.25 to 0.55 part of dispersant, 0.4 to 0.8 part of antifoaming agent, 0.05 to 0.25 part of multifunctional auxiliary agent, 0.05 to 0.15 part of antiseptic, 3 to 6 parts of titanium dioxide, 25 to 45 parts of filling material, 30 to 60 parts of emulsion, and 1 to 2 parts of rheological additive. The paint is prepared by a ternary compounding technology, which compounds three components: low-VOC pure acrylic emulsion, low-VOC vinyl acetate-ethylene emulsion, and soap-free organic silicon rubber emulsion; a VOC-free composite rheological system blending technology and a composite silver ion sterilizing and anticorrosion technology. The paint has the advantages of low VOC content, green, no toxicity, high strength, convenience in construction, and stableness in storage.