This work aims to provide a method for numerically and experimentally investigating the fracture mechanism of cement paste at the microscale. For this purpose, a new procedure was proposed to prepare micro cement paste cubes (100 × 100 × 100 µm³) and beams with a square cross section of 400 × 400 µm². By loading the cubes to failure with a Berkovich indenter, the global mechanical properties of cement paste were obtained with the aid of a nano-indenter. Simultaneously the 3D images of cement paste with a resolution of 2 µm³/voxel were generated by applying X-ray microcomputed tomography to a micro beam. After image segmentation, a cubic volume with the same size as the experimental tested specimen was extracted from the segmented images and used as input in the lattice model to simulate the fracture process of this heterogeneous microstructure under indenter loading. The input parameters for lattice elements are local mechanical properties of different phases. These properties were calibrated from experimental measured load displacement diagrams and failure modes in which the same boundary condition as in simulation were applied. Finally, the modified lattice model was applied to predict the global performance of this microcube under uniaxial tension. The simulated Young’s modulus agrees well with the experimental data. With the method presented in this paper the framework for fitting and validation of the modelling at microscale was created, which forms a basis for multi-scale analysis of concrete.