For the utilization of high-electron-mobility transistor (HEMT) devices fabricated on GaN on Si structure as high-power devices, deep pits, which are known as inverted pyramid-shaped defects formed in the surface of a HEMT structure, are critical because they act as leakage pathways and degrade the breakdown property. We investigated in detail the origin of pits in the HEMT structure with a strained-layer superlattice (SLS). The pits were found to emerge from rotation domains, in which the crystal structure rotates around the c-axis, in the AlN buffer layer. The analysis by ultra low voltage scanning electron microscopy (ULV-SEM) revealed that the domains were formed on dense Al regions in Al preseeding layer. By optimizing Al pre flow conditions, we eliminated dense Al regions in Al preseeding layer, consequently, no rotation domains in the AlN buffer layer. An extremely low pit density of the HEMT structure with fine breakdown property was successfully achieved.