The invention discloses a generation and transmission system operation reliability modeling and evaluation method considering primary and secondary frequency modulation. Firstly, in view of the problem that the existing system state analysis model does not consider primary frequency modulation of a wind turbine and secondary frequency modulation of an AGC unit, and after load shedding, the frequency is constantly kept at a lower limit, a load shedding optimization model considering a power flow model for primary frequency modulation of the wind turbine, the primary frequency modulation, the second frequency modulation and the minimum frequency deviation is provided; and on the basis, multiple uncertain factors such as the wind speed, the frequency modulation capacity of the wind turbine, the difference adjustment coefficient, element fault and load fluctuation are further considered, a generation and transmission system operation reliability evaluation method considering primary and secondary frequency modulation is provided, a frequency operation reliability evaluation index is built, and the possibility and the severity of frequency exceeding limit are reflected comprehensively; and finally, on an MATLAB platform, calculation and analysis on the generation and transmission system operation reliability evaluation considering primary and secondary frequency modulation are realized through a program.