In order to obtain a spectrum with high mass accuracy, an internal calibration of Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) is inevitable. This in turn is critical for subsequent data processing and is generally performed using the commercial instrument software DataAnalysis in the benchmark calibration mode. However, no methodological study has systemically addressed the automated internal calibration of FTICR-MS spectra for dissolved organic matter (DOM) from different sources such as terrestrial and aquatic environments. In this study, a new piecewise algorithm, FTMSCalibrate, was developed to automatically calibrate FTICR-MS spectra in both positive and negative ion modes. FTMSCalibrate was found to reproduce 91.7% ± 4.4% (referred to as the true positive ratio) of the chemical formulas obtained by calibration using manual DataAnalysis. In addition to significantly reducing the mass error, FTMSCalibrate is more accurate in terms of the molecular formula assignment for low m/z peaks than Formularity and MFAssignR. FTMSCalibrate was compatible with deprotonated ions for FTICR-MS spectra in the negative ion mode as well as protonated and adduct ions, including Na- and K-adducts, for FTICR-MS spectra in the positive ion mode. These results suggest that FTMSCalibrate publicly available herein is a robust alternative for the internal calibration of FTICR-MS spectra during postdata processing and will facilitate DOM analysis by FTICR-MS.