The Excitation-emission matrix (EEM) fluorescence spectra of dissolved organic matter (DOM) are not only dependent on the chemical structure of DOM as well as the local chemical environment around the DOM, but also dependent on the instrument employed for the analysis. Thus, in order to get the real spectra of the DOM, spectra correction of the effect of the instrument-specific response is necessary. However, some studies corrected DOM spectra, while still some studies didn’t, leading to inconformity when comparing the data and the results from different groups. The present work evaluated the effect of spectra correction on the fluorescence characteristics of DOM. The results demonstrated that DOM spectra differed significantly after correction. Fluorescence intensities showed a decrease in the range of Ex/Em=220~450/250~500 nm, while an increase at Em<250 nm after correction. Fluorescence intensity ratio (FI) and humification index (HIX) derived from peak picking method showed a decrease after correction, while biological index (BIX) increased slightly. PⅠ,n, PⅡ,n and PⅢ,n derived from FRI analysis exhibited a significant increase, while PⅣ,n and PⅤ,n decreased. The results suggest that spectral correction should be included when analyzing the properties and trends of the DOM using EEM.