Finite element-based digital volume correlation with mechanical regularization was utilized to measure the deformation fields in a concrete specimen under uniaxial compression based on in-situ (via microcomputed tomography) experiment. Heterogeneous and damage settings were introduced in the mechanical regularization. The mechanical response of the matrix and aggregates was investigated. The three-dimensional morphology of subvoxel microcrack openings was measured, the overall assessment and local depiction of concrete damage were quantified. Subvoxel microcrack openings greater than 0.26 vx were identified. The average maximum principal and average volumetric strains in the matrix were higher than those in the aggregates, and noticeable strain concentrations existed in the interfacial transition zone and pore edges. Microcracks initiated in the macroscopic elastic stage, whereas voxel-level crack openings were observed at 90% of the ultimate load. This study provides experimental support for further revealing the growth process of concrete damage.