In this work, we report the tunable emission properties of Ce3+ in an apatite-type LiY9(SiO4)6O2 compound via adjusting the doping concentration or temperature. The occupancies of Ce3+ ions at two different sites (Wyckoff 6h and 4f sites) in LiY9(SiO4)6O2 have been determined by Rietveld refinements. Two kinds of Ce3+ f-d transitions have been studied in detail and then assigned to certain sites. The effects of temperature and doping concentration on Ce3+ luminescence properties have been systematically investigated. It is found that the Ce3+ ions prefer occupying Wyckoff 6h sites and the energy transfer between Ce3+ at two sites becomes more efficient with an increase in doping concentration. In addition, the charge-transfer vibronic exciton (CTVE) induced by the existence of free oxygen ion plays an important role in the thermal quenching of Ce3+ at 6h sites. Because of the tunable emissions from cyan to blue with increasing temperature, the phosphors LiY9(SiO4)6O2:Ce3+ are endowed with possible thermometric applications.