Station autonomous computer system is the core of the centralized traffic control (CTC) system. The working mode is dual computer hot standby, and its reliability is very important. Due to the dynamic and fuzzy issue with the reliability analysis of station autonomous computer system, a reliability analysis method is formulated based on fuzzy dynamic fault tree (DFT) and Markov model. First, the structure and working principle of the dual computer hot standby autonomous computer system and the double 2‐vote‐2 autonomous computer system are analyzed, and two autonomous computer systems based on DFT are formulated. Then, the failure rates and the fault detection probabilities are considered as fuzzy variables and represented as triangular fuzzy variables. The fuzzy state transition matrix of the system is obtained by conversion of DFT to the Markov model. Finally, the fuzzy reliability of the system is calculated by Laplace transform. Simulation results show that the reliability of the dual computer hot standby autonomous computer system is higher than that of the double 2‐vote‐2 autonomous computer system. Besides, the reliability of the hardware system is not only related to the structure of the system, but also affected by the uncertain unit failure rate, fault detection probabilities, and so on.