The invention discloses a reactor core average axial direction flux deviation acquisition system, and belongs to the technical field of nuclear power station reactor core safety. The reactor core average axial direction flux deviation acquisition system comprises a reactor internal average axial direction flux deviation acquisition module, a reactor external average axial direction flux deviationacquisition module, a deviation term logic module, and a reactor core average axial direction flux deviation acquisition module; the reactor internal average axial direction flux deviation acquisitionmodule is used for acquiring current reactor internal average axial direction flux deviation compensation signals for positive input to the deviation term logic module; the reactor external average axial direction flux deviation acquisition module is used for acquiring current reactor external axial direction flux deviation signals, and negative input to the deviation term logic module after tautime delay; the reactor external average axial direction flux deviation acquisition module is used for acquiring current reactor external axial direction flux deviation signals for positive input to the reactor core average axial direction flux deviation acquisition module; and positive input of output signals of the deviation term logic module to the reactor core average axial direction flux deviation acquisition module is carried out. The reactor core average axial direction flux deviation acquisition system is capable of ensuring output of reactor core average axial direction flux deviationunder real-time calculating deviation item effective/ineffective states.