The heartbeat mechanism in Hadoop is not reasonable for short jobs, and ignores the fairness of expired time set of nodes in heterogeneous cluster. In order to overcome the problem, a fair expired time fault-tolerant mechanism was proposed. First of all, a failure misjudgement loss model and a Fair MisJudgment Loss (FMJL) algorithm were put forward according to reliability and computational performance of nodes, so as to meet requirements of the long jobs and short jobs at the same time. Then a fair expired time mechanism based on FMJL algorithm was designed and implemented. Running a 345 seconds short job on the Hadoop with the proposed fair expired time mechanism, the results showed that it saved completion time by 44% when there was fault on TaskTracker nodes, and saved completion time by 23% compared with self-adaptation expired time mechanism. The experimental results show that the proposed fair expired time mechanism shortens the fault-tolerant processing time without affecting the completion time of long jobs, and can improve the efficiency of real-time processing ability for a heterogeneous Hadoop cluster.