We have studied the electron mobility in the AlN/GaN/AlN heterostructures with the nanometer scale thickness by taking into account multiple quantized electron subbands and the confined optical phonon dispersion. It was shown that the inter-subband electronic transitions play an important role in limiting the electron mobility in the heterostructures when the energy separation between one of the size-quantized excited electron subbands and the Fermi energy becomes comparable to the optical phonon energy. The latter leads to the oscillatory dependence of the electron mobility on the thickness of the heterostructure conduction channel layer. This effect is observable at room temperature and over a wide range of the carrier densities. The developed formalism and calculation procedure are readily applicable to other material systems. The described effect can be used for fine-tuning the confined electron and phonon states in the nanoscale heterostructures in order to achieve performance enhancement of the nanoscale electronic and optoelectronic devices.