The growth conditions of the AlN nucleation layer (AlN NL) by focusing on the partial pressure of trimethyl aluminum (TMA) with a constant V/III ratio are optimized. The relationship between the size and the density of the surface pits of the AlN NL and the variation in the vertical‐direction breakdown voltage (VDBV) in the AlGaN/GaN high‐electron‐mobility transistor (HEMT) structure is determined. The maximum size of the pits in the surface of the AlN NL decreases as the partial pressure of TMA decreases. The density and the maximum size of the pits on the surface of the AlN NL decreased as the growth rate of AlN NL decreased. The pit density of the AlN NL decreases as the thickness of the AlN NL increased from 157 to 207 nm. Furthermore, the pit density is saturated when the thickness of the AlN NL was 207 nm. The optimum value of the thickness of AlN NL was about 200 nm. The variation in the VDBV of the HEMT structure decreases as the full width at half maximum (FWHM) of the rocking curve of the AlN (002) and AlN (102) planes, the pit density, and the maximum size of the pits in the AlN NL decrease. Thus, the variation in the VDBV of the HEMT structure can be related with the process of regrowth over the AlN NL.