In this contribution, the microstructure features of cement mortar exposed to various temperatures (105 °C, 200 °C, 400 °C, 600 °C, 800 °C) was investigated by combining Mercury Intrusion Porosimetry (MIP) and multi-scale X-ray computed tomography. The influence of exposure temperature and resolution of X-ray CT on the determination of microstructure parameters of heat-treated mortar was focused. Based on results of MIP test, it was found the porosity and pore size increased slightly when the exposure temperature varied from 105 °C to 200 °C and significant pore coarsening and micro-damage occurred once the temperature exceeded 400 °C. Bimodal pore size distribution (PSD) of the heat-treated mortar specimens was observed when the temperature reached 400 °C. To interpret the results of MIP test, the microstructure of heat-damaged mortar specimens was imaged using X-ray CT with a reconstructed voxel size of ~4.0 μm3 and then local volume inside the specimen was focused and scanned with a reconstructed voxel size of 1.5 μm3. A method was proposed to select proper threshold based on the MIP results for segmenting the void space from the X-ray CT images. The fracture aperture, 2D/3D fractal dimension, connectivity and tortuosity of the heat-damaged mortar specimens were further determined at different scale. By analyzing the fracture aperture determined from X-ray CT images, it was found the bimodal PSD revealed by MIP test can be associated with the creation of thermal micro-fractures. The fractal dimension increased remarkably when exposure temperature was raised from 400 °C to 600 °C while it varied slightly from 600 °C to 800 °C. Linear dependences between the fractal dimension and the volume fraction/tortuosity of micro-scale pores and fractures were found. The scale-dependent fractal properties of the heat-treated mortar were revealed with the capillary pressure data measured by MIP. The fractal dimension of micro-scale pores and fractures measured by MIP exhibited good consistency with that determined based on by X-ray CT images with a reconstructed voxel size of 1.5 μm3. •3D fracture aperture of heat-damaged mortar was presented at multi-scale.•Microstructure parameters measured by MIP and X-ray CT images with different voxel sizes were compared.•The connectivity, tortuosity and fractal features of micro-fractures were analyzed.