A scanning low-coherence heterodyne interferometer (SLHI) was developed for measuring the microstructural vibration inside the cochlear partition of the intact living cochlea of mice. The sensitivity, frequency response, and dynamic range of the SLHI are comparable with those of a sensitive laser interferometer but the SLHI has a higher spatial resolution along the optical axis. The magnitude and phase of sound-induced vibrations were measured as a function of the focal position along the optical axis. Our data show that the SLHI has sufficient sensitivity, dynamic range, and temporal and spatial resolution to measure sub-nanometer vibrations of the basilar membrane, reticular lamina, and tectorial membrane in the intact living mouse cochlea. High spatial and temporal resolution, compact heterodyne design, and scanning capability make this interferometer an ideal tool to study molecular mechanisms of hearing in normal and genetically-modified mice.