We present a method for 3D sub-nanometer displacement measurement using a set of differential optical shadow sensor. It is based on using pairs of collimated beams on opposite sides of an object that are partially blocked by it. Applied to a sphere, our 3-axis sensor module consists of 8 parallel beam-detector sets for redundancy. The sphere blocks half of each beam power in the nominal centered position, and any displacement can be measured by the differential optical power changes amongst the pairs of detectors. We have experimentally demonstrated a displacement sensitivity of 0.87 nm/rtHz at 1 Hz and 0.39 nm/rtHz at 10 Hz. We describe the application of the module to the inertial sensors of a drag-free satellite, which can potentially be used for navigation, geodesy and fundamental science experiments as well as ground based applications.