Building nanocrystalline–amorphous biphase nanostructure has recently emerged as an advanced route to improve radiation tolerance, as the nanocrystalline–amorphous interface is expected to enhance the sink efficiencies of helium atoms. However, the structure evolution and degradation mechanisms during helium ion implantation in nanocrystalline–amorphous biphase films are still unclear. This study aimed to further understand these mechanisms through in situ observation of nanocrystalline–amorphous TiAl biphase films deposited via magnetron sputtering in a helium ion microscope. Results demonstrate that during the helium implantation process (the final fluence was 4 × 1017 ions cm−2), a partial swelling occurred in the implantation region without blisters, cracks, or exfoliation on the surface. The AFM and TEM results revealed that the partial bulge originated from the differential in the swelling rate between the amorphous and grain areas during helium ion implantation. These findings offer promising insights into designing radiation-tolerant materials for advanced nuclear reactors.