The invention discloses a water-based wood protective agent. The water-based wood protective agent comprises methyltrimethoxysilane, hexadecyltriethoxysilane, ammonium hydroxide, benzalkonium bromide,alkaline silica sol, alkylphenol ethoxylates, sodium dodecyl benzene sulfonate and deionized water. A protective agent preparation method comprises the steps that (1) the methyltrimethoxysilane is added into the deionized water; (2) the sodium dodecyl benzene sulfonate is added; (3) the ammonium hydroxide is added; (4) hexadecyltriethoxysilane is added; (5) the alkaline silica sol is added into the deionized water; (6) the alkylphenol ethoxylates is added; (7) the benzalkonium bromide is slowly added into a solution obtained in the step (6); and (8) a solution obtained in the step (7) and a solution obtained in the step (4) are mixed and stirred. After wood is processed through the water-based wood protective agent, a compact breathing hydrophobic membrane is formed on the surface of wood, the wood is clear in texture, and the natural color of the wood is maintained. The water-based wood protective agent has the advantages of being non-poisonous, tasteless, transparent, resistant to water, mould, bacteria and ageing, simple in technology, low in cost and the like.