Oxyfluoride glass-ceramics with RF3 or NaRF4 (R3+: rare earth elements) nanocrystals are considered as favorable hosts for luminescence applications. In this work, we utilized large-scale molecular dynamics (MD) simulations with effective partial charge potentials to study a series of oxyfluoride glasses that are of interest to the precipitation of RF3 or NaRF4 nanocrystals as previous experiment results suggested. The results show that phase separation exists in all glass compositions with fluoride-rich regions made up of R3+, Na+, and F- and oxide-rich regions consisting of aluminosilicate networks. These fluoride-enriched regions can serve as the precursor for RF3, cubic and hexagonal NaRF4, and NaF crystal precipitation. The results also confirm that the concentration of Na+ in the fluoride phase plays a key role in determining the crystal phases (RF3, NaRF4, or NaF) and crystal structure (cubic vs hexagonal NaRF4) to be precipitated. Consequently, this study shows that MD simulations with effective potentials can fill the gap in the structural understanding of oxyfluoride glass and provide insights into atomic scale information of the phase separation behavior that is useful in predicting the potential crystal types in oxyfluoride glass. When coupled with experimental validations, these simulations can expedite the exploration of novel luminescent oxyfluoride glass ceramics.