The fluorescent spectra of amaranth and ponceau-4R have been measured by a fluorescence spectrophotometer. The result shows that ponceau 4R excited at 220～400 nm has four obvious fluorescence peaks at 420 nm, 530 nm, 635 nm and 637 nm respectively. Under the same condition, amaranth excited at 220～430 nm has only one obvious fluorescent peak at 654 nm. It is considered that the ponceau-4R′s four obvious fluorescence peaks are resulted from four fluorescent clusters. In order to find the sensitivity of every fluorescent cluster when excited by different-wavelength light, and the relation between the two pigments, the intensity of fluorescent peaks was calculated by matrix operation based on the principle of additive property of fluorescent intensity. The fluorescent peak of amaranth is found to be homologous to the third fluorescent peak of ponceau 4R. Based on this, the influence of four fluorescent clusters on two pigments′ fluorescent spectra was discussed. The origin of different fluorescence spectra was studied from the difference in the structure.