We report on the mechanism of strain-influenced quantum well (QW) thickness reduction in GaN/AlN short-period superlattices grown by plasma-assisted molecular beam epitaxy. Density functional theory was used to support the idea of a thermally activated exchange mechanism between Al adatoms and Ga surface atoms that is influenced by the strain state of the GaN QWs. These ab initio calculations support our experimentally observed reduction in QW thickness for different intrinsic strains.