As-deposited and unencapsulated GeTe1-xSex (x = 0, 0.5) 3-μm-thick amorphous films on Si(001) were obtained via the thermal co-evaporation technique. The crystallization and the structure of these phase change materials were examined using in situ temperature-dependent X-ray diffraction (XRD) and grazing-incidence fluorescence X-ray Absorption Near Edge Structure (XANES) in isochronal annealing conditions under nitrogen flow. The results show that the onset temperature of crystallization is highly sensitive to the substitution of the Te atoms by the Se ones and that the rhombohedral structure, with the space group R3m, is the one that crystallized for both samples without Ge or Te rejection. Moreover, the local order around the Ge and Se atoms, probed by Ge and Se K-edge XANES analyses, presents clear modifications from the amorphous state to the crystalline one expecting a Ge four-fold and a Se two-fold coordination in the amorphous state, with an increase of the local disorder with the Se substitution (x = 0.5).