Biochar-derived organic matter is key to carbon dynamics and pollutant transport in soils remediated by biochar. A limited understanding of the molecular composition of biochar-derived organic matter limits the ability to accurately predict the chemical cycle within soil and how biochar-derived organic matter will interact with contaminants. To describe the relatively comprehensive structure information of soybean straw biochar-extractable organic matter (BEOM) at the molecular level, we used solvents of different polarities, namely, petroleum ether (PE), carbon disulfide (CS2), methanol (CH3OH) and acetone (CH3COCH3), to extract organic samples from soybean straw biochar and used Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) for analysis. We found that a high percentage of unique molecular formulas were extracted by each solvent. This molecular diversity is mainly due to variance in solvent polarity and various intermolecular bonds destroyed by different solvents. The molecular signatures of the sub-fractions reveal that some recalcitrant BEOM sub-fractions will be easily released in the environment and preserved for a long time in the soil environment, while the majority of the labile BEOM sub-fractions tend to be preserved in the biochar itself. In addition, the most readily available organic N and S in biochar will be primarily released. These results reveal that biochar could provide nutrients efficiently and maintain soil organic carbon over the long term, suggesting that biochar is a promising material for soil improvement. By using high-resolution mass spectrometry, we revealed the BEOM signature at the molecular level in various possible environmental processes, which provides a theoretical basis for further research on the interactions between BEOM and organic contaminants.