An apparatus for controlling an amphibious vehicle includes an engine, a land propeller generating a propulsion force on land, a water propeller generating a propulsion force on water, a power distributor distributing power to the land propeller and the water propeller, a transmission for changing a shift ratio of the power supplied to the land propeller, and a controller, wherein the controller selects and executes one of a land mode for controlling travel on land, a water mode for controlling travel on the water, and a transition mode controlling the travel in a transition region, and the controller maintains an engine output torque in the land mode to be constant and maintains an engine output speed in the water mode and the transition mode to be constant.