Dissolved organic matter (DOM) has been used frequently to distinguish different environmental samples based on its abundant fingerprint information. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) is the most powerful technique to analyze the complex composition of DOM. Balancing between the reproducibility of peak magnitude and peak diversity is a key factor for achieving reliable and reproducible fingerprint information of DOM with FT-ICR-MS. In this paper, a novel magnitude filter (MGF) method and a novel MS-MGF strategy were proposed to improve the data reproducibility of FT-ICR-MS analysis. With the MS-MGF strategy, a 20% magnitude filter threshold (TMGF) was recommended to remove magnitude outliers, and a relatively low signal-to-noise ratio (SNR) threshold of 3.5 was recommended to retain those low but stable-magnitude peaks. The total relative magnitude was recommended since it could obtain better reproducibility of MS analysis compared to other types of peak magnitude. In addition, three replicates were enough to obtain satisfactory reproducibility. More importantly, the proposed MS-MGF strategy was also adaptable to different FT-ICR-MS instruments and different experimental conditions. Overall, the results are expected to initiate the promising applications of the MS-MGF strategy to distinguish the reliable fingerprint characteristics of DOM samples from different sources.