The influence of concrete meso-structure and coarse aggregate size on early age crack is studied. In this study, concrete is regarded as a three-phase material based on shrinkage property. The mortar matrix and interfacial transition zones undergo shrinkage and no spherical coarse aggregate particles are considered to restain the shrinkage by particle interaction. The results show that concrete meso-structure plays an important role in the safety of concrete, different aggregate distribution in concrete leads to different initial cracks and propagation due to shrinkage. With the increase of maximum aggregate size, the value of shrinkage deformation becomes unstable and varies in a wide range; relevant shrinkage cracking becomes easier too.