The composition, structure, and thermal behaviors of yttrium-containing phosphate glasses were studied in this work, and the glass-ceramics were prepared via the two-step crystallization method. The XRD and SEM-EDS results show the forming range of the phosphate glass system and the formation of YPO4 (xenotime) due to the addition of excessive Y2O3. The spectroscopic characterization of these glasses presented shifts of the infrared and Raman bands, demonstrating the depolymerization of the glass network and the formation of novel P–O–Y bonds, and the deconvoluted Raman spectra also exhibited the occurrence of the disproportionation reaction in the glass melting process. The content of non-bridging oxygen (NBOs) from the UV–vis spectra first increased and then decreased with increasing Y2O3. The thermal behaviors show that the Y2O3 reduced the crystallization peak temperature and the thermal stability of the glasses. The crystalline behaviors of the phosphate glass matrix were investigated at different crystallization times of 2–10 h, and a transformation of the crystallization mechanism from surface to volume crystallization was found. The yttrium phosphate glass-ceramics crystallized for 10 h exhibited transformation of the main crystalline phases with increasing Y2O3, and the grain-oriented crystalline surface became irregular.