An object of the invention is to provide a floating mobile object control system capable of causing a floating mobile object to stand still in a predetermined position with high precision or track a target trajectory with high precision, even under disturbances caused by waves, tidal current, etc.A floating mobile object control system of the present invention capable of achieving the above object is a control system 1 for a floating mobile object 10, in which the floating mobile object includes: a main body part B that can be considered as a single rigid body constituting a part of the floating mobile object; an effector part E for generating a thrust for the floating mobile object; and a thrust transfer gate G for dynamically connecting the main body part and the effector part, the thrust transfer gate being adapted to be able to actually measure a thrust from the effector part acting on the main body part, and a measured value for the thrust from the thrust transfer gate G is used to obtain a thrust command to the effector part E (FIG. 4).