Hovering performance of unmanned helicopter is of key importance in flight.This paper presents an autonomous control system to achieve the excellent hovering performance for a miniature unmanned helicopter. First, the response data of system is collected during special flight test and a linear time-invariant model is extracted by frequency identification technique.Then, the control system is designed and implemented on hover control of the helicopter using multi-loop control method. The method has simple structure, straightforward design process and low computing load imposed on the flight control system. The proposed multi-loop controller is composed of inner-loop attitude control, mid-loop velocity control and the outer-loop position control. The application results show that the proposed controller can obtain outstanding hovering performance. This control system structure is very feasible in engineering, and can be benefit for control system design of other miniature unmanned helicopters.