Network management is one of the important issues of network researches. This work investigates and implements a network management system with the following properties: cross-layer design and automatic management. While exceptions occur, most previous management systems rarely take both layer-two and layer-three into consideration at the same time; this work provides cross-layer design solutions which is more efficient and flexible under heterogeneous network environments. After some experiments in practical environments, this system can quickly diagnoses and deal with problems, such as abnormal used IP addresses, worms and unusual connections therefore save managers a lot of time.