We investigate the effect of an ultra-thin AlN/GaN superlattice interlayer (SL IL) on the GaN epilayer grown on Si(110) substrates by metalorganic chemical vapor deposition (MOCVD). It is found that micro-cracks (MCs) are self-generated in the SL IL region, which depend on the thickness of the SL IL. The MCs influences the characteristics of the GaN epilayers grown on the SL IL, such as surface morphologies, strain and structural qualities. Furthermore, different MCs configurations depending on the SL IL thickness are observed, which imply the controllability of the MCs generation. The mechanism understanding and the optimization of the SL IL structure make it possible to grow crack-free high-quality GaN films on Si substrates for optic and electronic device applications.