The invention belongs to the technical field of hydrophobic treatment on surface of glass, and particularly relates to a high-transparency glass hydrophobic agent and a preparation method thereof. Thehigh-transparency glass hydrophobic agent is prepared from the following raw materials in parts by weight: 100 parts of dimethylcyclosiloxane, 20-50 parts of phenylsiloxane, 5-10 parts of a silane coupling agent, 0.1-1 part of an alkaline catalyst, 5-100 parts of a nonionic surfactant and 10-90 parts of a solvent. A transparent hydrophobic film can be formed on the surface of glass, when water issprayed on the surface of the glass, water drops are formed, a contact angle reaches up to 110 degrees, the dropping speed of the water drops is greatly increased, and the water drops can automatically roll off without marks, so that the problem of unclear line of sight is solved.