The key system which requiring very high levels of reliability often use redundancy to enhance reliability index, e.g. tolerant system. During system operation, tolerant system monitors system state and reconfigures it to realize continuous working with system drawback. Considering the inevitable errors in system online test and the performance degradation, an estimation method for both system reliability and performance is proposed in this paper. Through analyzing the important fault mode in tolerant system, establishing the system reliability model based on k-out-n:G system description, and then considering the imperfect tests and corresponding performance degradation in these process, the reliability and performance evaluation method is given, moreover, the engineering operation flow of this method was established for it. An aircrafts rudder system is taken as an example for engineering application, which shows that this approach is feasible and effective.