When Energy-Dispersive X-RayFluorescence(EDXRF)used for measuring cerium (Ce) content in the Bayan Obo ores, matrix effect mainly comes from iron (Fe) and calcium (Ca). Due to extensive concentration variability of the two elements, commonly employed standard sample method for matrix effect correction is invalid. To overcome the problem, testing samples were prepared based on the average contents of elements in the Bayan Obo ores, and the influence of Fe and Ca on the coefficient in a linear relationship between Ce content and XRF signal was determined by linear least squares fitting for multivariate analysis. The coefficients thus determined reflected the matrix effect on Ce emitted fluorescence from Fe emitted fluorescence and Ca absorption. When the coefficients were used in analyzing Ce content in Bayan Obo mine by EDXRF, the relative error is less than 10%.