A method of fabricating an organic thin film transistor is disclosed, which comprises steps of (S1) forming a gate electrode on a substrate; (S2) forming a gate insulating layer on the gate electrode; (S3) providing a gas on the surface of the gate insulating layer to form hydrophobic molecules on the surface of the gate insulating layer; (S4) forming an organic semiconductor layer, a source electrode, and a drain electrode over the gate insulating layer having hydrophobic molecules thereon, wherein the gas of step (S3) is at least one selected from the group consisting of halogen-substituted hydrocarbon, un-substituted hydrocarbon, and the mixtures thereof. The method of the present invention utilizes gases comprising carbon or fluorine atom to perform surface treatment on the surface of the gate insulating layer, therefore the hydrophobic character of the surface of the gate insulating layer can be enhanced and the electrical properties of the OTFT can be improved. Also, a method of surface treatment for the gate insulating layer is disclosed.