The invention discloses antibacterial water-based ink and a preparation method thereof. The antibacterial water-based ink comprises components in parts by weight as follows: 20-60 parts of an acrylic resin liquid, 10-30 parts of organic pigments, 10-20 parts of deionized water, 15-20 parts of ethyl alcohol, 0-10 parts of an antibacterial agent and 0-2 parts of filler and an auxiliary, wherein the antibacterial agent is one or more of nano-copper oxide, nano-cuprous oxide, nano-copper, nano-silver or nano-gold containing functional surface groups. The antibacterial agent is modified and is enabled to contain the functional surface groups, so that hydrophilicity of the antibacterial water-based ink is improved, and the stability of the antibacterial water-based ink is improved; besides, the antibacterial agent contains the functional surface groups, and accordingly, the antibacterial water-based ink has excellent oxidation resistance and antibacterial performance, and the content of heavy metal is low.