The invention discloses an automatic generation control (AGC) signal disturbance processing system of a large-scale thermal power generating set. The signal disturbance processing system comprises a power grid dispatching center, a power plant remote terminal unit RTU and a power plant automatic generating control system. The power grid dispatching center transmits an AGC signal to the power plant automatic generating control system through the RTU. The signal disturbance processing system further comprises a subtraction module, an absolute value module, an upper pound module, a NOT gate module M5, a digital quantity time-delay module, a NOT gate module M8, an analog quantity switching module M9 and an analog quantity switching module M12. Through the connection of parameters and the modules, small-fluctuation interference signals in the small-fluctuation interference AGC signals received by a power plant set are disposed of, the quality of supplied power is improved from the source, and the availability ratio index of power plant set AGC check is increased.