The invention relates to a water-based electromagnetic wave shielding coating and a preparation method thereof. The water-based electromagnetic wave shielding coating is prepared from a water-soluble hybrid material loaded with metal nanoparticles, water-soluble resin, a silane coupling agent, white carbon black, a water-based crylic acid dispersion agent, an antifoaming agent, water and ethyl alcohol. The water-soluble hybrid material loaded with the metal nanoparticles is prepared from carrier molecules A, stabilizer molecules B and the metal nanoparticles. The preparation method of the water-based electromagnetic wave shielding coating comprises the steps that the water-soluble hybrid material loaded with the metal nanoparticles, water and the silane coupling agent are fully mixed, and then the mixture, water and an ethyl alcohol mixing solvent are mixed to prepare a component B; water-soluble resin, white carbon black, the dispersion agent, the antifoaming agent, water and the ethyl alcohol mixing solvent are fully mixed to prepare a component A; the component A and the component B are mixed to be uniform, and the water-based electromagnetic wave shielding coating is obtained. The preparation method is simple in process and easy to operate, and the water-based electromagnetic wave shielding coating achieves the shielding effectiveness being -50 dB or above within the use frequency range of 50 MHz to 2,000 MHz.