Microstructures of stacked silicon-nitride/amorphous-silicon/crystalline-silicon (SiNx/a-Si/c-Si) layers prepared by catalytic chemical vapor deposition were investigated with scanning transmission electron microscopy to clarify the origin of the sensitive dependence of surface recombination velocities (SRVs) of the stacked structure on the thickness of the a-Si layer. Stacked structures with a-Si layers with thicknesses greater than 10 nm exhibit long effective carrier lifetimes, while those with thin a-Si layers have very short effective carrier lifetimes. A remarkably close correlation was found between the dependence of interface structures on the thicknesses of a-Si layers and the SRVs. In samples with a-Si layers less than 10 nm thick, significant damage occurred in c-Si wafers close to the interfaces, while those near a-Si layers larger than 10 nm remained nearly defect-free during observations over long periods. The observation of stacked structures without an SiNx layer, along with energy dispersive spectroscopy and secondary ion mass spectroscopy analyses of nitrogen atom distributions, suggest that the preferential damage in c-Si wafers with thin a-Si layers is caused by nitrogen atoms in the interface regions of c-Si wafers that diffuse during the growth of SiNx layers.