The invention provides an environment-friendly water-based transparent primer. The primer is prepared from, by weight, 25-45% of fluorine-carbon modified acrylic emulsion, 15-25% of styrene-acrylic emulsion, 0.3-0.5% of wetting dispersant, 10-15% of talcum powder, 5-10% of water-based zinc stearate powder, 4-10% of a film forming auxiliary agent, 0.2-0.6% of thickener, 1-3% of an antifreezing agent, 0.3-0.6% of anticorrosion bactericide, 0.3-0.5% of a antifoaming agent, 0.3-0.5% of a flatting agent, 0.2-0.6% of a PH adjusting agent and 4-16% of water. The environment-friendly water-based transparent primer is good in color, transparency and glossiness and low in cost; a paint film of a product is short in drying time, good in transparency, high in glossiness and excellent in mechanical property; the invention further provides a preparation method of the transparent primer, the preparation method is simple in process, easy to operate and good in repeatability, and the product is short in production cycle, high in production efficiency and quite suitable for industrialized production.