Corneal biomechanics play a critical role in maintaining corneal shape and thereby directly influence visual acuity. However, direct corneal biomechanical measurement in-vivo with sufficient accuracy and a high spatial resolution remains an open need. Here, we developed a three-dimensional (3D) motion-tracking Brillouin microscope for in-vivo corneal biomechanics mapping. The axial tracking utilized optical coherence tomography, which provided a tracking accuracy better than 3 µm. Meanwhile, 10 µm lateral tracking was achieved by tracking pupils with digital image processing. The 3D tracking enabled reconstruction of depth-dependent Brillouin distribution with a high spatial resolution. This superior technical performance enabled the capture of high-quality mechanical mapping in vivo even while the subject was breathing normally. Importantly, we improved Brillouin spectral measurements to achieve relative accuracy better than 0.07% verified by rubidium absorption frequencies, with 0.12% stability over 2000 seconds. These specifications finally yield the Brillouin measurement sensitivity that is required to detect ophthalmology-relevant corneal biomechanical properties.