The invention discloses a method and system for filtering malicious traffic in an autonomous domain. The method comprises the following steps of acquiring network information and node state information of node equipment in a current network in real time, and generating a global unified real-time information view according to the information; constructing a filtering strategy module based on an Exception-Handler strategy module; instantiating the filtering strategy module according to the type of the malicious traffic and the type of a filter node in the network; and based on the instantiated filtering strategy module, using a filter node search algorithm to deploy the instantiated filtering strategy module to the filter node of the network to realize the filtering of the malicious traffic. The method for filtering the malicious traffic in the autonomous domain provided by the invention has greater advantages in the aspects of scope of protection, flexibility and expandability on the premise of realizing effective filtering of the malicious traffic in the network, and has a good application prospect.