To solve the problems of relationship between efficiency and security in traditional WWW intrusion tolerant system, a multilevel intrusion toleration mechanism was proposed. First, each web document had corresponding security level which was classified by its size and sensitivity. The initial grading factor was specified and dynamically adjusted by the security risks of web documents. Additionally, by the coefficient of Logistic equation, the uncertainty and initial value sensitivity of chaotic system was used to generate the chaotic fragment and its signature according to the initial grading factor. Even if the integrity of the web documnet requested by user was destroyed, the mechanism can also trigger a series of intrusion toleration oprarions include detecting the intrusion, denying the invalid access, alerting and renewing the system, etc. Because the chaotic intial value was produced randomly and chaotic system had character of initial value sensitivity, the chaotic fragment according to the chaotic intial value was uncertain. The invader was difficult to forged the signature of the chaotic fragment. The experiments showed that the security mechanism can carry a better balance between security and efficiency.