A model reference adaptive controller for a twin rotor multiple-input multiple-output system is considered in this article. The objective is to make the twin rotor multiple-input multiple-output system move quickly and accurately to the desired attitudes specified by a reference model. Because of the coupling influence between the two axes of the twin rotor multiple-input multiple-output system and its nonlinear complexity, the controller design is performed on the vertical plane and horizontal plane separately. Thus, the nonlinear multiple-input and multiple-output model of the twin rotor multiple-input multiple-output system is decoupled into two subsystems, and the cross-couplings are considered as disturbances to each other. The obtained two models are transformed via Lie derivatives to a canonical form required for adaptive controller design. Then, a hyperstability-based adaptive control technique is applied for each subsystem. The proposed controller design is evaluated in simulations of cross-coupled condition. The obtained results show that the controlled system is robust against disturbances with high tracking performance.