The invention discloses an intelligent nanometer blocking agent for water-based drilling fluid and a preparation method thereof. The intelligent nanometer blocking agent is prepared from, by weight, 20-82 parts of intelligent polymer-modified magnetic nanoparticles, 3-45 parts of polyethylene glycol and 0.5-24 parts of polytetramethylene glycol. The preparation method includes the steps that the intelligent polymer-modified magnetic nanoparticles are added into water, polyethylene glycol is added with constant stirring, the mixture is subjected to a reaction for 3-5 hours, polytetramethylene glycol is added, the mixture is subjected to a reaction for 4-7 hours, water is evaporated, the product is dried for 4 hours at 60-75 DEG C, and then the intelligent nanometer blocking agent for the water-based drilling fluid is obtained. The preparation method has the advantages that the hydrophilia and hydrophobicity of the intelligent nanometer blocking agent can change correspondingly along with different formation temperatures and drilling fluid pH values, so that in the shale formation drilling process, while micro pores in the well wall are physically blocked, a water molecule repelling effect is achieved, water is chemically restrained from approaching the well wall, and then the water blocking performance of the drilling fluid is significantly improved.