The beneficial role played by non-conductive film (NCF) under-fill (UF) compared with the conventional capillary under fill (CUF) is meticulously investigated for the reliability issues in high-density 3D-integration at die/wafer-level. The NCF with co-efficient of thermal expansion (CTE) value of 35 ppm/°C tremendously reduces the local deformation of 20 pm-thick three-dimensionally (3D)-stacked LSI die/wafer. This reduces the local mechanical stress in thinned 3D-LSI by nearly 5 times as against the CUF with the CTE value of 60–70 ppm/C. Both μ-RS and μ-XRD data showed only ∼250 MPa of tensile stress on the back surface of 20 pm-thick stacked die/wafer with NCFUF, whereas it was more than five-times larger (∼1400 MPa) for CUF. μ-XRD data illustrates that the cause for residual stress in the bump-space region and above the μ-bump are respectively due to the lattice tilt and change in lattice space.