The microcapsule-contained self-healing materials are appealing since they can heal the cracks automatically and be effective for a long time. Although many experiments have been carried out, the influence of the size of microcapsules on the self-healing effect is still not well investigated. This study uses the two-dimensional discrete element method (DEM) to investigate the interaction between one microcapsule and one microcrack. The influence of the size of microcapsules is considered. The potential healing time and the influence of the initial damage are studied. The results indicate that the coalescence crack is affected by the size of holes. The elastic modulus, the compressive strength and the coalescence stress decrease with the rising radius of holes. The initial damage in experiments should be greater than 95% of the compressive strength to enhance the self-healing effect. The large microcapsules require slight initial damage. Both a new type of displacement field near the crack and a new category of coalescence crack are observed. The influence of sizes of holes on the cracking behavior of concrete with a circular hole and a pre-existing crack is clarified.