The invention relates to a water-based low smoke low toxicity thin type fire resisting coating for a steel structure and a preparation method thereof, which belongs to technical field of coating. The invention aims to improve the main performance indexes of the prior thin type fire resisting coating for the steel structure such as fire resisting performance, bond strength, water resistance, cold and hot cycle resistance, and the like, and reducing the quantity and toxicity of the flue gas produced by the coating reacting with fire. The water-based low smoke low toxicity thin type fire resisting coating for the steel structure comprises the following components: water soluble acrylic ester emulsion, low sulfur expandable graphite, ammonium polyphosphate, wollastonite, spherical closed pore expanded perlite, a filler and an additive. The preparation method comprises the following steps: 1, mixing and grinding ammonium polyphosphate, wollastonite, the filler and water soluble acrylic ester emulsion; 2, adding water soluble acrylic ester emulsion, low sulfur expandable graphite, spherical closed pore expanded perlite and the additive, and agitating the raw materials evenly; and 3, adding water to adjust the viscosity of the coating. The invention is suitable for the coating carrying out the fire resisting protection on the steel structure and the preparation method thereof.