The insulator/semiconductor interface structure is the key to electric device performance, and much interest has been focused on understanding the origin of interfacial defects. However, with conventional techniques, it is difficult to analyze the interfacial atomic structure buried in the insulating film. Here, we reveal the atomic structure at the interface between an amorphous aluminum oxide and diamond using a developed electron energy analyzer for photoelectron holography. We find that the three-dimensional atomic structure of a C− O−Al−O−C bridge between two dimer rows of the hydrogenterminated diamond surface. Our results demonstrate that photoelectron holography can be used to reveal the three-dimensional atomic structure of the interface between a crystal and an amorphous film. We also find that the photoelectron intensity originating from the C−O bonds is strongly related to the interfacial defect density. We anticipate significant progress in the study of amorphous/crystalline interfaces based on their three-dimensional atomic structures analysis.