Microcapsule-based self-healing concrete (MSC) has been widely studied, with a focus on static behavior and self-healing effectiveness. However, the dynamic mechanical properties of MSC have rarely been studied. This study presents a mesoscale numerical investigation of the dynamic compressive behavior of MSC under impact loading. In mesoscale, MSC is regarded as a four-phase composite material mainly composed of coarse aggregates, interface transition zones, cement mortar, and microcapsules. A pseudo 3D numerical model is constructed by combining a slice of a detailed mesoscale model with a homogenous 3D model. The mesoscale MSC slice models with different mass fractions of microcapsules (0%, 2%, 5%, and 8%) are constructed. Different coarse aggregate shapes (i.e., circles, ellipses, and polygons) are considered. The uniaxial dynamic compressive behaviors of MSC materials under loads of different strain rates are numerically simulated and compared with those from split Hopkinson pressure bar tests previously done by the authors. The comparison results show that the present mesoscale model can accurately predict the compressive strength and failure mode of MSC. The effects of the microcapsules ratio and strain rate on the dynamic strength are studied. Results show that the MSC compressive strength decreases with the increase in microcapsules and increases with the increase in strain rate. The dynamic increase factor (DIF) of the specimen is jointly contributed by the material DIF, inertial constraints, and heterogeneity. Different aggregate shapes have little effect on the simulation results of MSC behavior. The obtained dynamic mechanical properties of MSC may assist in designing MSC to resist collisions or explosions.