Natural organic matter (NOM) is a complex organic mixture and plays a crucial role in environmental processes. By using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), detailed molecular information on NOM could be achieved. In this paper, ion accumulation time (IAT), a key parameter of FTICR-MS for complex mixture detection, was the focus, and its effect on the molecular characterization of NOM by FTICR-MS was systematically investigated. A notable feature of selective detection of NOM molecules by FTICR-MS with different IAT was observed. Most of the polar molecules with high O/C ratio (O/C ratio >0.5) could be easily detected by FTICR-MS with a short IAT, but extending IAT led to the ion intensities of these molecules decreasing or even disappearing. Meanwhile, a large number of unsaturated and aromatic molecules with low O/C ratio (O/C ratio <0.6) and low polarity, all of which could not be observed with a short IAT, were remarkably detected by extending IAT. Results also revealed that the unsaturated and aromatic molecules, which could only be observed by extending the IAT, were not generated by the fragmentation of molecules in NOM or from the dissociation of NOM aggregations but originally existed in NOM samples. The selective detection of NOM molecules caused by IAT extension was possibly attributed to their different polarity and different stability in the collision cell. On the basis of these results, a novel strategy of combining mass spectrometric data of NOM obtained with different IAT by FTICR-MS was proposed. With this strategy, more than 4715 CHO-molecular formulas were assigned, where about 2000 more formulas were obtained in comparison with using a short IAT (2733 CHO-molecular formulas identified) solely. The strategy is simple and robust and can be used as an alternative method to obtain more molecular information on NOM in the environment.