In this paper, we propose a new approach to the autonomous and high-speed indoor navigation of wheeled mobile robots using hybrid system controller. The hierarchical structure of hybrid system presented consists of high-level reasoning process and the low-level motion control process and the environmental interaction. In a discrete event system, the discrete states are defined by the user-defined constraints and the reference motion commands are specified in the abstracted motions. The hybrid control system applied for the nonholonomic mobile robots can combine the motion planning and autonomous navigation with obstacle avoidance in the indoor navigation problem. For the evaluation of the proposed algorithm, the algorithm is implemented to the two-wheel driven mobile robot system. The experimental results show that the hybrid system approach is an effective method for the autonomous navigation in indoor environments.