We describe a general, physics-based approach to numerical reconstruction of the geometrical structure and mechanical properties of natural sedimentary rock in 3D. Our procedure consists of three main steps: sedimentation, compaction, and diagenesis, followed by the verification of rock mechanical properties. The dynamic geologic processes of grain sedimentation and compaction are simulated by solving a dimensionless form of Newton’s equations of motion for an ensemble of grains. The diagenetic rock transformation is modeled using a cementation algorithm, which accounts for the effect of rock grain size on the relative rate of cement overgrowth. Our emphasis is on unconsolidated sand and sandstone. The main input parameters are the grain size distribution, the final rock porosity, the type and amount of cement and clay minerals, and grain mechanical properties: the inter-grain friction coefficient, the cement strength, and the grain stiffness moduli. We use a simulated 2D Fontainebleau sandstone to obtain the grain mechanical properties. This Fontainebleau sandstone is also used to study the initiation, growth, and coalescence of microcracks under increasing vertical stress. The box fractal dimension of the micro-crack distribution, and its variation with the applied stress are estimated.