Study on the atomic stacking configurations and grain boundary structures of ultrathin nanocrystalline TiN films deposited by the atomic layer deposition technique reveals that the dangling bonds and surface reconstruction may be the intrinsic factors that result in the crystal growth with different configurations. The surface topography of the amorphous SiO2 layer is an extrinsic factor to affect the atomic stacking configurations in ultrathin nanocrystalline TiN films. The analysis indicates that the coherent boundary should be the favored boundary in the connection of the tilt grains. These atomic stacking and grain boundary configurations may be the main factors to produce the pinhole-free, high-density, and homogeneous ultrathin nanocrystalline TiN film prepared by the atomic layer deposition method. This study may provide new insight into the fundamental mechanism and properties of ultrathin TiN films.