The invention relates to a preparation method of a transparent super-hydrophobic zinc oxide coating on a glass substrate. The preparation method comprises the following steps of a, substrate pretreatment; b, zinc oxide solution preparation; c, zinc oxide coating preparation; and d, zinc oxide coating surface modification. Compared with the prior art, the preparation method has the beneficial effects of simple equipment process, low cost and mild reaction condition and is beneficial to large-scale industrial production. The transparent super-hydrophobic zinc oxide coating prepared by using the method has excellent hydrophobicity and transparency; the contact angle is larger than 160 degrees, the rolling angle is smaller than 8 degrees, and water drops can freely roll on the coating, so that the transparent super-hydrophobic zinc oxide coating has relatively good self-cleaning performance; and the light transmittance is approach to 90% which is close to that of blank glass, so that the transparent super-hydrophobic zinc oxide coating has favorable visible light transmittance. A surface modifier used in the preparation method is an alkyl silane coupling agent instead of a fluorinated compound, so that the cost is low, the environment pollution is relatively low, and the modified coating is relatively stable.