The Ba8.8Ce0.1Na0.1Y2Ge6O24 orthogermanate phosphor, prepared by LiCl flux assistance under a reducing atmosphere, exhibited a mysterious green-yellow emission at 298 K. A blue-emitting orthogermanate phosphor was expected to be achieved through the lower d-band of Ce3+ ions in the host structure owing to their optical structure geometry. Oxygen vacancies were observed in the phosphors through investigating bond-length fluxations, the oxygen 1s profile, and the Ge2+/Ge4+ oxidation state, using synchrotron X-ray diffraction refinement, X-ray photoelectron spectroscopy, and Ge K-edge X-ray absorption near-edge structure spectra, respectively. The Ba-M4,5 edge shift, bonding limitation, and distortion index discovery reveal the oxygen-coordinating environment variation around the Ba2+(Ce3+) ions in the phosphors. The green-yellow emission results from the active 6-coordinated antiprism oxygen geometry around the Ce3+ ions in the phosphors.