Based on the three dimensional fluorescence spectra (EEMs) technology combined with the parallel factor analysis (PARAFAC), the spectral characteristics and sources analysis of dissolved organic matter of two rainstorms were investigated for different rainfall duration and molecular weight organic carbon in Zhoucun Reservoir. Two humic-like substances (C1, C2), one fulvic-like substance (C3) and two protein-like substance (C4, C5) were identified by PARAFAC model, and there exhibited significantly correlation coefficient in C1 & C2/C3/C4/C5, C2 & C3 and C3 & C4/C5, respectively. For the same molecular weight organic carbon, total dissolved organic matter (DOM) fluorescence intensity and the fluorescence intensity of each component showed a decreasing trend with the increase of rainfall duration and exhibited significantly differences distribution in two rainstorms. For the same rainfall duration, the total fluorescence intensity of the first rainstorm increased with the decrease of molecular weight organic carbon, while the total fluorescence intensity of the second rainstorm decreased with the decrease of molecular weight. The two rainstorms water both exhibited strong autochthonous component characteristics and first rainstorm exhibited strong terrestrial input characteristic; C1 and C3 exhibited significantly correlation coefficient with nitrate, ammonia, total nitrogen and organic carbon. From all the results, the study could supply a strong support for the managers of Zhoucun Reservoir to explore the DOM characteristic of rainstorm in the future.