with the rapid development of information technology especially Ipv6, people become more and more dependent on internet and some related applications. yet some security intrusion vary from minor mischief for pleasure, denial of service, and criminal intent for stealing or destroying still threat the security of information system which provides service online. Traditional researches on intrusion tolerant mainly focus on Ipv4, which cannot satisfy the requirement of Ipv6. Regarding this problem, the architecture of intrusion tolerant system based on Ipv6 is designed and some critical modules are improved accordingly, the workflow of the system is described in detail. The validity of the system is proven by the result of simulation experiment.