The color center and optical characteristics of Yb:YAG transparent ceramic were investigated for various cation additives (Si4+, Mg2+ and Si4++Mg2+). The presence of a population of free electrons in the vacuum sintered Yb:YAG ceramics without additives, which imparted a green color and promoted the formation of Yb2+-F+ centers. The introduction of Si4+ additives were unable to remove the [Yb2+-F+] composite color centers. Theoretical analysis and experimental proofs revealed that the cation additives containing ions aliovalent to YAG introduces vacancies, which in turn induce the formation of Re2+-F+ (Re2+: Yb2+, Mg2+ or Ca2+) composite color centers. It was also demonstrated that the addition of a combination MgO+SiO2 sintering aid serves to inhibit abnormal grain growth and enhance densification, accompanied with the elimination of color centers. Furthermore, the underlying mechanisms by which these aliovalent cation additives influence color center formation and optical properties are discussed in detail. The lowest optical attenuation loss was measured at 1064nm in Yb:YAG ceramic with the MgO+SiO2 additives, to be 0.0031cm−1, a value close to that observed for single crystals.