In order to solve the problem that it is difficult to accurately determine the crystal composition, a method for the accurate determination of crystal composition by X-ray fluorescence spectrometry with YAG crystal as the standard sample is developed. The samples are pure YAG crystal, and the doping concentration of raw materials with 1.2 at% and 2.0 at% Yb:YAG crystals. The composition of Yb: YAG crystals with different concentration is determinedby X-ray fluorescence spectrometry. Using pure YAG crystal as the standard sample, the accuracy of the detection results is greatly improved. The detection error of main components Y3+ and Al3+ is less than 1%, and that of Yb3+ is less than 5%. The results show that the segregation coefficient of Yb3+ in the crystal are 1.025 and 1.045, which are close to 1. It is conducive to the realization of high concentration doping and high quality crystal growth of Yb:YAG crystal. The doping concentration difference of 2.0 at% Yb:YAG crystal is less than 5%, which indicates that the doping concentration uniformity of equal diameter part is high.