Optical dephasing of Pr3+ and Tm3+ ions doped in transparent oxyfluoride glass ceramics was studied with the two-pulse photon echo technique. It was found that the dephasing time of rare earth ions is dramatically less in nanocrystals embedded in a glass matrix than in bulk crystals. A quasi-linear temperature dependence obtained at low temperatures proved that the long-range interaction of the ions inside the nanocrystals with the two level systems of the glass matrix dominates the optical dephasing. The local thermal effect in glass ceramics containing nanocrystals elevates the local temperature, which results in the reduction of optical dephasing time. For Tm(3+)-doped glass ceramics, the elevation of local temperature induced by the irradiation of excitation laser even quenched the photon echo signals in the experimental study.