In the present paper, British Edinburgh FLS920P Steady State and Time-Resolved Fluorescence Spectrometer was applied to measure three dimensional fluorescence spectra of 12 pigment solution samples and the parallel factor algorithm was combined with the excitation-emission matrix to find a way to detect the food colors. In the experiment, making use of CORCONDIA determination method to confirm that the number of the components is 3 in mixed solution, and then by using parallel factor analysis (PARAFAC) algorithms, get the average recoveries of carminum and Allura red were 99.3% +/- 5.0% and 102.2% +/- 5.6%, and the root mean square errors of prediction (RMSEP) were 0.054 and 0.205, respectively. The results show that the method can be applied to determine carminum and Allura red in the mixed solution simultaneously even in the presence of interfering amaranth, which was simple and convenient, rapid, etc, and provides references for synthetic food pigments detection.