Microalgae are an attractive feedstock for biofuel production thanks to their renewable nature, high growth rate, and ability to use anthropogenic CO2. The conversion of microalgae by hydrothermal liquefaction (HTL) leads to a solid residue, a gaseous phase, and a biocrude. However, the bio-oil is rich in heteroatoms and requires upgrading processes to be used as biofuels. For these treatments to be effective, detailed knowledge of the sample is crucial. The bio-oil was characterized by direct introduction into a Fourier transform ion cyclotron resonance mass spectrometer (DI-FTICR MS) with an electrospray ionization source (ESI). Thousands of molecular formulas were assigned with a high level of confidence, mainly compounds with nitrogen and oxygen atoms. Additionally, the bio-oil was analyzed by coupling supercritical fluid chromatography (SFC) and FTICR to combine the separation power of SFC to the high performances of a 12 T FTICR. Quadrupole detection (2ω) was used in FTICR to have a high resolving power with a lower transient time. The coupling allowed the separation of many isomers along the chromatogram, showing the isomeric complexity of microalgae bio-oils. Moreover, classes of compounds were separated according to their heteroatom class thanks to the SFC separation. In this work, the advantages of DI-FTICR MS and SFC-FTICR MS proved complementary, and DI was useful to study the bio-oil at the molecular scale thanks to the high performances, while SFC proved useful for the characterization at the isomeric scale. This demonstrated the significant potential of this new online hyphenated technique for the characterization of complex matrices.