There are many problems during the preparation of the scintillation crystal Gd₃(Al,Ga)₅O₁₂:Ce (abbreviated as GAGG:Ce), such as inclusions and antisite-defect. In order to inhibit these defects and obtain large-size and high-quality GAGG:Ce crystal, this study uses Gd₃(Al,Ga)₅O₁₂ as the matrix and Ce³⁺ as the doping ions to grow the GAGG:Ce crystal by the Czochralski method. The phase structure, micro-region composition, optical and scintillation properties of GAGG:Ce are tested and compared. It is found that tipical Ce³⁺ absorption bands are at 340 nm and 440 nm, and the linear transmittance at 550 nm is 82%. The transmittance of the crystal tail drops to about 70% due to the macroscopic defects such as inclusions. The micro-region composition analysis shows that the three types of inclusions in GAGG:Ce crystal are Gd-rich phase, Ce-rich phase, and (Al,Ga)₂O₃ phase. The Ce³⁺ ion emission wavelength of GAGG:Ce crystal is about 550 nm excited by the X-ray, and there is also an emission wavelength caused by the Gd_Al/Ga antisite-defect at 380 nm. The emission intensity of Gd_Al/Ga antisite-defect in the lack of (Al,Ga) component is higher than that in the excess (Al,Ga) component. The inclusions and Gd_Al/Ga antisite-defect make the luminous efficiency of GAGG:Ce crystal decrease by 12.5% and the corresponding light yield decreases from 58500 to 52000 photon/MeV. The tunneling effect between Gd_Al/Ga antisite-defect ions and neighboring Ce³⁺ ions makes the decay time of the GAGG:Ce crystal extend from 117.7 to 121.9 ns, and the ratio of slow component increases from 16% to 17.2%. The migration of energy along the Gd³⁺ sublattice makes the rise time of the GAGG:Ce crystal extend from 8.6 to 10.7 ns. The above conclusions further deepen the understanding of the source of inclusions and the relationship between the Gd_Al/Ga antisite-defect and crystal composition, and provide a theoretical basis for restraining the defects and improving the crystal properties.