Two different of Sm-loading fluorapatite (Ca10−2xNaxSmx(PO4)6F2, x = 1 and 2) glass-ceramics were synthesized by a two-step melt sintering method. The samples were irradiated with 50 keV He+ ions with a fluence of 2.6 × 1016 ions/cm2 at 593 K. The irradiation induced microstructural evolution were characterized by grazing incidence X-ray diffraction and cross-sectional transmission electron microscopy. For the smaller Sm-doping samples, no phase transformation is observed. Meanwhile, in the lager Sm-doping samples, the irradiation induced the crystals into smaller nanocrystals. The mechanism of the transformation of the crystalline phase was also analyzed and discussed.