The secondary system of the smart substation has numerous components with complex structure, thus the state space with establishing directly may yield dimensionality disaster. It is difficulty to derive the analytical expression about the sensitivity of the system state probability to the reliability parameters of its components, thus the risk analysis of each component cannot be obtained directly. In this paper, the method of reliability equivalence is introduced to obtain the complete state space of the secondary system of the smart substation. The state spaces of its subsystems are established, and combined by the method of frequency and duration (F D), yielding the reliability model of the whole system. For the weakness analysis of the secondary system of the smart substation, the matrix description of the F D method is applied in this paper to obtain the connection of between the transition rates before and after the equivalence, deriving the analytical expression about the partial derivative of the system state probability to the reliability parameters of its components, which helps to quantify the corresponding sensitivities. The numerical results give the results of the reliability and sensitivity, which provide the reference to the weakness analysis of the secondary system of the smart substation.