Featured with dynamic, system complexity, maintainability and dependency across successive mission phases, space TT&C system ensures the stable and safe operation for any aerospace project, and its reliability is very important. Regarding the characteristic of space TT&C system, a Markov-based reliability analysis method is presented. In this method, TT&C is treated as a multiple phases mission system, with states keep unchanged in the same mission period, while there possibly exist changes across the different periods. According to the time variant dynamic reconfiguration characteristics, process of internal state transfer in each task stage is described using Markov model, through the Kolmogorov backward equation, the state probability of the system at the mission completion time is calculated, and the dependency between two task stages is fully considered with state mapping by probability theory. Consequently, the whole reliability of the system is derived by solving all the mission stages altogether. The method is proved with high precision and reliable. Finally, an example is given to show the validity of the algorithm through comparing with that of Monte Carlo-based method.