Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) has been widely applied to characterize the molecular compositions of dissolved organic matter (DOM) in diverse ecosystems, providing crucial information for understanding the origin, migration, transformation, and degradation of DOM. Most previous research has explored the molecular composition characteristics of DOM from just one or a few ecosystems, and the lack of large-scale DOM composition comparisons across diverse ecosystems prevents us from obtaining a better understanding by which we can trace the molecular compositions of DOM from different sources and further explore its biogeochemical cycling across ecosystems. In this study, a total of 67 DOM samples from 13 ecosystems are analyzed using negative-ion electrospray ionization FT-ICR MS. The results show that the molecular compositions of DOM from diverse ecosystems are dramatically different. Most average molecular parameters can reflect ecosystem characteristics to a large extent, implying valuable geochemical information obtained by FT-ICR MS. However, the variation patterns of some molecular parameters in this study are not entirely consistent with the previous research, partially due to the limited number of samples from each ecosystem type. Therefore, a larger and more comprehensive FT-ICR MS molecular fingerprint database is needed to better constrain the generalizability of the differential features among ecosystems. Meanwhile, it is necessary to improve the mass spectrometry analysis method to allow the characterization of differences in DOM compositions from different sources with the compositional information of specific groups of “signature molecules”.