The invention discloses a self-aligned graphene field effect transistor and a manufacturing method thereof. The self-aligned graphene field effect transistor comprises a semiconductor substrate, an insulating layer, a conducting channel, a source electrode, a drain electrode, a gate dielectric layer, gate metal, self-aligned metal, the insulating layer is formed on the semiconductor substrate, the conducting channel is is formed on an insulator and formed by graphene, the source electrode and the drain electrode are formed on two sides of the conducting channel respectively, the gate dielectric layer selectively deposits on the conducting channel between the source electrode and the drain electrode, the gate metal is formed on the gate dielectric layer, and the gate dielectric layer and the gate metal are simultaneously and graphically piled together to form a gate accumulation layer to control carrier concentration of a channel area. A self-aligned metal layer covers on the source electrode, the drain electrode, the conducting channel and the gate metal, so that the area of a region not being covered by a grid and self-aligning of a device grid and the source electrode as well as the drain electrode is realized.