The invention relates to the field of petroleum drilling, and particularly discloses a nanometer plugging agent and a preparation method thereof. The nanometer plugging agent is prepared from the following raw materials in parts by weight: 10 to 50 parts of vinyl monomer, 10 to 25 parts of allyl monomer, 5 to 15 parts of sodium methacrylate sulfonate, 2 to 10 parts of an emulsifier, 1 to 1.5 parts of an initiator, 15 to 55 parts of water, 5 to 10 parts of an organic emulsion, 15 to 25 parts of a filler and 5 to 10 parts of sepiolite. The organic emulsion is prepared from the following components in parts by weight: 1 to 1.5 parts of polylactic acid, 0.5 to 1 part of lignocellulose, 1 to 4 parts of stannic chloride, 0.3 to 0.5 part of sodium dodecyl benzene sulfonate, 0.1 to 0.2 part of benzimidazole, 0.5 to 1 part of gelatin, 2 to 3 parts of dimethyl sulfoxide and 1 to 1.5 parts of white oil. The nanometer plugging agent can plug micro-nano gaps, acting force between nano-particles and the stratum is large, the nano-particles are not prone to being separated from the gaps, a plugging rate is high, and high temperature resistance is high.