The physical properties of a doped quantum dot (QD) 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 wave functions of the host lattice. Although several synthetic methodologies have been developed for introducing dopants inside the size-confined semiconductor nanocrystals, the controlled dopant-host lattice coupling by dopant migration is still unexplored. In this work, the effect of lattice mismatch of CdS/ZnS core/shell QDs on Mn(II) dopant behavior was studied. It was found that the dopant migration toward the alloyed interface of core/shell QDs is a thermodynamically driven process to minimize the lattice strain within the nanocrystals. The dopant migration rate could be represented by the Arrhenius equation and therefore can be controlled by the temperature and lattice mismatch. Furthermore, the energy transfer between host CdS QDs and dopants can be finely turned in a wide range by dopant migration toward the alloyed interface during ZnS shell passivation, which provides an efficient method to control both the number of the emission band and the ratio of the emission from the host lattice and dopant ions.