The invention discloses a smart substation communication system reliability and flexibility analysis method and system applied to a smart substation communication system. The method includes 1, establishing a reliability indicator system; 2, establishing an original parameter system; 3, establishing a flexibility system; 4, acquiring a system state space model; 5, acquiring original parameters; 6, acquiring reliability indicators; 7, calculating the flexibility; 8, analyzing the flexibility; 9, providing reliability improving measurement advances; 10, completing the flexibility analysis, and implementing the reliability and flexibility analysis method. The flexibility of the smart substation communication system is analyzed, the weak link of the smart substation communication system can be found out, and the reliability of the smart substation communication system can be improved.