•Micro-CT has been used to investigate various cement-based materials.•Threshold determination from micro-CT images is crucial for phase identification.•Microstructure and property relations are effectively correlated through micro-CT. Cement-based materials are generally highly heterogeneous, and their material properties are strongly affected by the characteristics and spatial distributions of each constituent. However, it is difficult to characterize the compounds inside these materials without destroying them. Micro-computed tomography (micro-CT) is an approach that enables the investigation of the inner structure of a material without damaging the specimen. From micro-CT, a series of cross-sectional images of a material with a pixel size of a few micrometers can be achieved, which can be used to evaluate the characteristics of the material. In this study, the use of micro-CT for various cement-based materials, e.g., lightweight concrete and high-performance concrete, is summarized. The characteristics of pores and solid phases, such as the volume fraction and spatial distribution, are also analyzed, and their relations with the physical properties of cement-based materials are reviewed and presented. It is shown that micro-CT has a great potential not only for investigating the performance of existing materials but also for developing new cement-based materials.