An oxygen-incorporated Mo silicide layer was explored to form the Mo nanocrystals after rapid thermal annealing. Transmission electron microscopy showed the nanocrystals embedded in SiOx. Charge-storage characteristics of Mo nanocrystals influenced by Mo oxide and its surrounding oxide were investigated through X-ray photoelectron spectroscopy and electrical measurement. X-ray photoelectron spectral analyses revealed a redox reaction in the oxygen-incorporated Mo silicide layer after rapid thermal annealing at a critical temperature. The memory window and retention were improved because of the reduction of Mo oxide. Furthermore, the double-layer nanocrystal structure was fabricated through the annealed stacked oxygen incorporated Mo silicide layer. A larger memory window and long retention were found for the double-layer nanocrystal structure. We used an energy band diagram to explain the difference in retention characteristics between single- and double-layer structures.