Spectral smoothing is commonly used as effective pretreatment methods in the spectral analysis. However, the conventional Savitzky-Golay polynomial smoothing methods used in two-dimensional spectral analysis can not be applied to three-dimensional spectrometry directly. In the present paper, a polynomial surface smoothing method is proposed, and the two-dimensional Savitzky-Golay polynomial smoothing methods are extended to three-dimensional fluorescence spectra. Experiment for detecting dissolved organ matter in water using three-dimensional fluorescence spectrometry was carried out, and experimental results show that the smoothing method for the three-dimensional fluorescence spectrum can effectively improve the modeling accuracy.