Nanocrystalline materials containing amorphous intergranular films (AIFs) exhibit excellent mechanical properties, radiation resistance, and thermal stability, which may serve as promising candidate materials in advanced nuclear energy systems. Here, we aim to unveil the effect of mechanical stress on the radiation damage behavior of the AIF systems. Based on a bi-crystal Cu system with Zr-doped AIFs, we use molecular dynamics to simulate the radiation process, and examine the AIF sink efficiency, defect propensity, defect size distribution, and Zr mixing under uni-axial and hydrostatic strain conditions.We found the sink efficiency of the glue-like AIFs is not compromised with the applied strains. The anisotropy resulting from the intrinsic microstructure and elastic deformation leads to distinct radiation response, where extension (contraction) of the structure perpendicular to AIFs increases (decreases) vacancy density. The strain dependent defect density, along with the cluster size distributions can be interpreted from variations in defect formation energy and anisotropic defect diffusion. Finally, the Zr mixing induced by collision cascades is found insensitive to the mechanical strains. These findings provide meaningful information towards understanding the stress effect on the radiation response of AIF systems.