The invention discloses a method for preparing a coating on the surface of a hydrophobic insulating layer. The method includes the following steps that the hydrophobic insulating layer is prepared on a base material; coating paint is added to the hydrophobic insulating layer; electrowetting processing is conducted, that is, proper voltage is applied on the position between the base material and the coating paint, the electrowetting effect is utilized, and the surface of the hydrophobic insulating layer becomes wettable; coating is conducted. The method can be used for preparing coatings on the surface of various hydrophobic insulating layers, such as, electrowetting display, micro-fluidic chips, electrowetting sensing, electrowetting micro lens and electrowetting micro electro mechanical system and the application range of hydrophobic insulating materials can be greatly expanded.