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Space tracking, telemetry, and command (TT&C) system can be viewed as a phased-mission system (PMS). Markov model for TT&C system reliability analysis was proposed based on Fault Tree model of all mission stages. To overcome the difficulty of the computational complexity and ensure computational accuracy in large TT&C system, a Runge-Kutta algorithm was presented. Numerical examples demonstrate that the proposed algorithm has high accuracy for system of various scales.