The invention discloses a debugging method and system for a closed-loop control system of a nuclear power plant. The debugging method comprises the following steps: A, a parameter design value input in an off-line checking table by a user is received to generate a checking message; B, a control parameter of a PID (Proportion Integration Differentiation) controller is verified and adjusted according to the checking message; C, the verified and adjusted control parameter is optimized under a disturbance operating condition; D, the control parameter of the PID controller and/or the logic and related constant value of the PID controller are/is modified under an instantaneous condition so as to ensure the normal response of the closed-loop control system under the instantaneous condition. According to the technical scheme disclosed by the invention, the debugging risk of the closed-loop control system is reduced, the debugging cycle of the closed-loop control system is shortened, the operation quality of a unit is improved, and good economic benefits are obtained.