The invention relates to an optimizing method of air and flue gas system control after desulfurization and denitrification transformation of a thermal power generating unit. An oxygen amount allowancecontrol loop after desulfurization and denitrification transformation of the thermal power generating unit and a loop interface, a secondary air valve opening degree allowance control loop after desulfurization and denitrification transformation of the thermal power generating unit and a loop interface, an induced draft fan output allowance control loop after desulfurization and denitrification transformation of the thermal power generating unit and a loop interface as well as a booster fan output allowance control loop after desulfurization and denitrification transformation of the thermal power generating unit and a loop interface are additionally arranged in the control logical configuration of a thermal power generating unit distributed control system (DCS); air blower output interlocking control logic and secondary air valve opening degree interlocking control logic after desulfurization and denitrification transformation of the thermal power generating unit are added in the control logical configuration of the thermal power generating unit DCS; according to the real-time running curve of the control system, related parameters of various control loops for optimization of airand flue gas system control after desulfurization and denitrification transformation of the thermal power generating unit are adjusted online, and the expected control effect is realized finally. Theproblem about automatic air and flue gas system control after desulfurization and denitrification transformation of the thermal power generating unit is solved, the equipment potential is fully played, and the stability of main parameters is guaranteed.