We study the formation of stars with varying amounts of heavy elements synthesized by the rapid neutron-capture process (r-process) based on our detailed cosmological zoom-in simulation of a Milky Way–like galaxy with an N-body/smoothed particle hydrodynamics code, asura. Most stars with no overabundance in r-process elements, as well as the strongly r-process-enhanced (RPE) r-II stars ([Eu/Fe] > +0.7), are formed in dwarf galaxies accreted by the Milky Way within the 6 Gyr after the Big Bang. In contrast, over half of the moderately enhanced r-I stars (+0.3 < [Eu/Fe] ≤ +0.7) are formed in the main in situ disk after 6 Gyr. Our results suggest that the fraction of r-I and r-II stars formed in disrupted dwarf galaxies is larger the higher their [Eu/Fe] is. Accordingly, the most strongly enhanced r-III stars ([Eu/Fe] > +2.0) are formed in accreted components. These results suggest that non-r-process-enhanced stars and r-II stars are mainly formed in low-mass dwarf galaxies that hosted either none or a single neutron star merger, while the r-I stars tend to form in the well-mixed in situ disk. We compare our findings with high-resolution spectroscopic observations of RPE metal-poor stars in the halo and dwarf galaxies, including those collected by the R-Process Alliance. We conclude that observed [Eu/Fe] and [Eu/Mg] ratios can be employed in chemical tagging of the Milky Way’s accretion history.