Uncertainties parameters of section carrying capacity calculation in speed restriction conditions are analyzed. The capacity calculation method based on Fuzzy Markov Chain is established according to its characteristics of dynamic, fuzziness, randomness and non after effect property. The section carrying capacity in emergency is expressed by fuzzy random variable, which remains the randomness of capacity changing with the impact of emergencies and the fuzziness of the driving behavior and other factors. The case study on Beijing Shanghai Highspeed Line shows that the capacity calculation method based on Fuzzy Markov Chain reflects the capacity dynamic process in emergency. It has an excellent fault tolerance of a variety of factors and uncertainties and provides a wealth of options for policy makers. The capacity calculation gives consideration to a variety of typical transport organization strategies, such as the jacobinical, the conservative or the compromised scheme, which is more coincident with the actual operation of the train in special conditions.