The UAV (Unmanned Aerial Vehicle) performs various kinds of missions while performing autonomous flight navigation. In order to realize all functionalities of the UAV, the software part becomes a very complex hard real-time system because some hard real-time tasks, soft real-time tasks and non-real-time tasks are concurrently working together under a RTOS. In this paper, a hierarchical architecture for Unmanned Autonomous Helicopter System is proposed that guarantees the real-time performance of hard real-time tasks and the re-configurability of soft real-time or non-real-time tasks under the RT-Linux. This software architecture has four layers: hardware, execution, service agent and remote user interface layer according to the reactiveness level for external events. In addition, the layered separation of concurrent tasks makes different kinds of mission reconfiguration possible in the system. An Unmanned autonomous helicopter system was implemented using Kyosho RC Helicopter to test and evaluate the performance of the proposed systems.