In an apparatus for controlling a small boat having a hull and two outboard motors mounted on a stern of the hull and an actuator adapted to open/close a throttle valve of each engine of the motors for regulating speed of the engine, acceleration acting on the boat in a direction of gravity axis when the boat ascends or descends the ocean wave and angular acceleration about the gravity is detected and a correction amount of the engine speed is calculated based on the detected acceleration so as to change behavior of the boat, thereby mitigating a burden on the operator and improving stability of the boat.