More and more studies are based on digital microstructures of cement pastes obtained either by numerical modelling or by experiments. A comprehensive understanding of the their pore structures, therefore, becomes significant. In this study, the pore structure of a virtual cement paste (HYMO-1d) generated by cement hydration model HYMOSTRUC 3D is characterized. The pore structure of HYMO-1d is compared to the one of CT-1d that is reconstructed by using X-ray computed tomography technique (CT scan). Both HYMO-1d and CT-1d have the same porosity. Various parameters are taken into account, viz., the specific surface area, the pore size distribution (PSD), the connectivity and the tortuosity of water-filled pores. Regarding the PSD, two concepts (i.e., the “continuous PSD” and the “PSD by MIP simulation”) are adopted. The “continuous PSD” is believed to be a “realistic” PSD; while the “PSD by MIP simulation” is affected by the “throat” and “ink bottle” pores. The results show that HYMO-1d and CT-1d exhibit a similar curve of “continuous PSD”, but distinct curves of “PSD by MIP simulation” and different specific surface areas. A lower complexity of the pore structure of HYMO-1d is indicated by a higher tortuosity of water-filled pores with reference to CT-1d. This study indicates that the comparison of pore structures between the digital microstructures should be based on multiple parameters. It also gives an insight into further studies on digital microstructures, i.e. transport properties of unsaturated materials.