An in situ study is reported on the structural evolution in nanocluster films under He+ ion irradiation using an advanced helium ion microscope. The films consist of loosely interconnected nanoclusters of magnetite or iron-magnetite (Fe-Fe3O4) core-shells. The nanostructure is observed to undergo dramatic changes under ion-beam irradiation, featuring grain growth, phase transition, particle aggregation, and formation of nanowire-like network and nanopores. Studies based on ion irradiation, thermal annealing and electron irradiation have indicated that the major structural evolution is activated by elastic nuclear collisions, while both electronic and thermal processes can play a significant role once the evolution starts. The electrical resistance of the Fe-Fe3O4 films measured in situ exhibits a super-exponential decay with dose. The behavior suggests that the nanocluster films possess an intrinsic merit for development of an advanced online monitor for fast neutron radiation with both high detection sensitivity and long-term applicability, which can enhance safety measures in many nuclear operations.