This paper develops a three-dimensional (3D) microscopic model to investigate the mechanical response of cement mortar with random defects at high strain rates. Ellipsoids with randomness in size, shape, and spatial distribution are used to simulate the defects in mortar matrix. First, we propose the steps to generate the ellipsoid. Second, a “take and place” algorithm is employed to generate a model of cement mortar composed of defects. The mapping algorithm is used to generate a finite-element grid. In finite-element modeling, the material model is used in an advanced general-purpose multiphysics simulation software package to simulate the nonlinear behavior of mortar matrix with strain rate effects. Numerical simulations of the specimen under static loadings agree well with test observations, which reveal that the proposed 3D microscopic model and finite-element analytical approach can give reliable predictions. Finally, numerical studies are conducted, focusing on the effect of the defects on ...