The emissions of Ce3+ in Ce:YAG are at approximately 550 nm and are generated by the overlapping emission of two transitions 5d →2F5/2 (2F7/2), and their luminescence characteristics are markedly influenced by temperature and ion fluence. In this study, the temperature and ion fluence dependence of Ce3+ emission was investigated using ion beam-induced luminescence (IBIL) at four different temperatures (25, 150, 300, and 450 °C), and potential theoretical explanations for the variation were discussed. Experimental results show that (1) as the temperature increases, the intensity of Ce3+ decreases, and the central peak position continues to redshift; (2) as the temperature rises, the proportion of the high-energy peak at approximately 2.3 eV continuously increases; (3) a double exponential model can describe the evolution of the Ce3+ luminescence intensity with fluence; and (4) the influence of 2 MeV H+ on the luminescence characteristics of Ce:YAG is limited. The luminescence characteristics of the Ce:YAG single crystal deteriorate when exposed to high temperatures. Combined with the observed experimental phenomena, we recommend that the practical operating temperature of the Ce:YAG single crystal in a high ion fluence environment should be as low as 150 °C when possible to ensure a high scintillation yield and good luminescence performance.