The 3D local atomic structures and crystal defects at the interfaces of heterostructures control their electronic, magnetic, optical, catalytic and topological quantum properties, but have thus far eluded any direct experimental determination. Here we determine the 3D local atomic positions at the interface of a MoS2-WSe2 heterojunction with picometer precision and correlate 3D atomic defects with localized vibrational properties at the epitaxial interface. We observe point defects, bond distortion, atomic-scale ripples and measure the full 3D strain tensor at the heterointerface. By using the experimental 3D atomic coordinates as direct input to first principles calculations, we reveal new phonon modes localized at the interface, which are corroborated by spatially resolved electron energy-loss spectroscopy. We expect that this work will open the door to correlate structure-property relationships of a wide range of heterostructure interfaces at the single-atom level.