To investigate the micro-mechanical properties of calcium sulfoaluminate cement and the correlation with the microstructures, we apply a variety of advanced techniques of microstructural and micro-mechanical characterization, including scanning electron microscopy with backscattered electron and energy-dispersive X-ray spectroscopy detectors, X-ray fluorescence, X-ray diffraction and nanoindentation. For the first time, the micro-mechanical properties of material microstructures present in a calcium sulfoaluminate cement are estimated. In the calcium sulfoaluminate cement used in this research, two type of hydration product microstructures with the differentiable microstructural morphologies, compositions and micro-mechanical properties are identified and investigated. The correlation of the micro-mechanical properties with the microstructures shows that the hydration product microstructure containing more ettringite has lower indentation modulus and hardness than that containing more aluminum hydroxide.