The phosphors Y6MoO12:Eu3+ have been synthesized via citrate complexation method at different calcination temperatures. The evolutions of the crystal structure and the photoluminescence (PL) properties were characterized by means of powder X-ray diffraction (XRD), Raman and PL spectra, respectively. It was revealed that a red emission could be obtained via three excitation channels, namely f-f transition of Eu3+ ions, charge-transfer transition from O-2 to Eu3+, and interband transition (IBT) of MoO6 groups. The PL spectra and their temporal decay character of Eu3+ ions depended on both crystal structure and excitation channel. The emission reduced with the crystallite size when Eu3+ ions were excited directly, but the emission evolved in a different model with the host lattices were excited. The effect of grain boundary and other lattice defect on the energy transfer and dissipation within the phosphors were discussed.