We propose an extrinsic Fabry-Perot interferometer (EFPI)-based optical fiber sensor with a novel mechanical design for nano-scale strain measurement. In our proposed sensor, a designed mechanical structure consists of a cylinder and a square column attached to a stainless steel substrate. This simple and compact structure along with a fiber ceramic ferrule and a gold-coated reflective mirror as a packaged EFPI sensor can resolve nano-scale strain with temperature self-compensation. In comparison with the existing nanostrain sensing methods, no reference sensors and complicated configurations are needed. The strain measured by our proposed sensor ranges from 0 to 677 nε with a measurement accuracy of ±5 nε. This robust and easy-to-build geometry-based nano-scale strain sensor has great potential in nanotechnology, geophysical research, seismic monitoring, and other practical applications.