Aiming at the problem of hovercraft formation–containment control with compound perturbations including model uncertainties and ocean disturbances, a distributed control algorithm for underactuated hovercraft formation–containment is proposed by combining adaptive linear extended state observer (ALESO) and radial basis function neural network (RBFNN). Firstly, ALESO and RBFNN are designed to estimate the ocean disturbances and model uncertainties, respectively, for dynamic compensation in the controller. Then, the auxiliary variables are introduced into the formation error function, and the lateral and longitudinal error stabilization is transformed into the design of longitudinal force and rotational torque by using the skew-symmetric matrix transformation, which solves the lateral underactuated problem of the hovercraft. Finally, the uniform ultimate boundedness of formation–containment cooperative errors is proved by the Lyapunov stability theory. Digital simulation verifies the effectiveness of the proposed method.