The rod shadow effect of the mechanical shim of PWR nuclear power plant causes the axial flux deviation (AFD) indicated by the protection system to become the weighted value of peripheral components rather than the average value of the core. Therefore, the control system based on the average AFD of the core cannot directly use the output value of the protection system like the traditional power plant. Based on this problem, several linear indication ways of core average AFD of control system are explored, the effects of different control rod positions and xenon oscillation transient on linear relationship are studied, and a core average AFD calibration method with “deviation correction” is proposed. Through the verification of the unit peak shaving process, the results show that the method can eliminate the influence of the control rod position, the unit power change and the xenon concentration change on the AFD indication of the control system, and can meet the requirements of the system indication accuracy. Therefore, this method can be used for the calibration of the mechanical shim control system AFD.