The present paper proposes a new method to find the ratio of three-dimensional fluorescence peak. At first, the excitation-emission fluorescence matrix of water samples was treated with parallel factor analysis (PARAFAC) and then fluorescence peaks intensity and ratio of fluorescence peak were obtained from the parallel factor analysis model. From the parallel factor analysis model, the same fluorescence peaks of different water samples lie at the same excitation-emission wavelength and the overlap of different fluorescence peaks of the same water sample is reduced. Analysing regional characteristic in Taihu Lake, the ratio of factor score and the ratio of fluorescence peak showed strong correlation.