Semiconductor nanocrystals(NCs) with size-tunable luminescence are one of the most interesting materials capturing the interest of researchers over the past decades, and have broad applications in biological imaging, drug delivery, light-emitting devices, solar cells, photo-detectors, and quantum computing. Doping of transition metal ions into semiconductor NCs is a thriving area of nanomaterials because it can introduce new optical, electronic, and magnetic properties into host NCs. The physical properties of a doped NCs are strongly influenced by the dopant site inside the host lattice, which determines the host–dopant coupling from the overlap between the dopant and exciton wavefunctions of the host lattice. In our work, the effect of internal composition of the host NCs and temperature Mn(II) dopant behavior was studied. It was found that the dopant can migrate toward the local lattice sites with smaller cationic size mismatch between the dopant and host lattice, which is a thermodynamically driven process to minimize the lattice strain from the size mismatch. Controlling dopant site by migration offers a rigorous and rational approach to design functional NCs with unprecedented properties, and provides new fundamental understanding of dopant site-dependent properties of NCs.