Metal–oxide–semiconductor capacitors made of the nanocrystalline ruthenium oxide embedded Zr-doped HfO2 high-k film have been fabricated and investigated for the nonvolatile memory properties. Discrete crystalline ruthenium oxide nanodots were formed within the amorphous high-k film after the 950 °C postdeposition annealing step. The capacitor with the Zr-doped HfO2 high-k gate dielectric layer traps a negligible amount of charges. However, with the nanocrystalline ruthenium oxide dots embedded in the high-k film, the capacitor has a large memory window. The charge trapping capacity and the trapping site were investigated using the constant voltage stress method and the frequency-dependent capacitance–voltage measurement. The memory function is mainly contributed by the hole-trapping mechanism. Although both holes and electrons were deeply trapped to the bulk nanocrystalline RuO site, some holes were loosely trapped at the nanocrystal/high-k interface. The current–voltage and charge retention results confirmed the above-mentioned charge trapping mechanism. In summary, this kind of nanocrystal-embedded high-k dielectric has a long charge retention lifetime, which is suitable for future nanosize nonvolatile memory applications.