Metal-oxide interfaces with poor coherency have unique properties comparing to the bulk materials and offer broad applications in the fields of heterogeneous catalysis, battery, and electronics. However, current understanding of the three-dimensional (3D) atomic metal-oxide interfaces remains limited because of their inherent structural complexity and limitations of conventional two-dimensional imaging techniques. Here, we determine the 3D atomic structure of metal-oxide interfaces in zirconium-zirconia nanoparticles using atomic-resolution electron tomography. We quantitatively analyze the atomic concentration and the degree of oxidation, and find the coherency and translational symmetry of the interfaces are broken. Atoms at the interface have low structural ordering, low coordination and elongated bond length. Moreover, we observe porous structures such as Zr vacancies and nano-pores and investigate their distribution. Our findings provide a clear 3D atomic picture of metal-oxide interface with direct experimental evidence. We anticipate this work could encourage future studies on fundamental problems of oxides such as interfacial structures in semiconductor and atomic motion during oxidation process.