A multifunctional switch system for an autonomous vehicle may include a plurality of docking stations in the interior of the autonomous vehicle, sets an operation mode of a mobile operation device for each of positions of the plurality of docking stations, and operates in an operation mode corresponding to the position of the docking station as the mobile operation device is docked to the docking station to enable a driver in the autonomous vehicle to conveniently operate various convenience devices regardless of the driver's location, and an operating method thereof.