Bio-oils obtained by thermochemical or biochemical conversion of biomass represent a promising source of energy to complement fossil fuels, in particular for maritime or air transport for which the use of hydrogen or electricity appears complicated. As these bio-oils are very rich in water and heteroatoms, additional treatments are necessary before they can be used as biofuel. In order to improve the efficiency of these treatments, it is important to have a thorough knowledge of the composition of the bio-oil. The characterization of bio-oils is difficult because they are very complex mixtures with thousands of compounds covering a very wide range of molecular weight and polarity. Due to the high degree of orthogonality between the two chromatographic dimensions, the on-line combination of reversed-phase liquid chromatography and supercritical fluid chromatography (on-line RPLC x SFC) can significantly improve the characterization of such complex matrices. The hyphenation was optimized by selecting, in SFC, the stationary phase, the co-solvent, the make-up solvent prior to high resolution mass spectrometry (HRMS) and the injection solvent. Additionally, a new interface configuration is described. Quality descriptors such as the occupation of the separation space, the peak shapes and the signal intensity were considered to determine the optimal conditions. The best results were obtained with bare silica, a co-solvent composed of acetonitrile and methanol (50/50, v/v), a make-up solvent composed of methanol (90%) and water (10%) with formic acid (0.1%), an addition of co-solvent through an additional pump for SFC separation in a 2.1 mm column, and an hydro-organic solvent as injection solvent. The optimized setup was used to analyze two microalgae bio-oils: the full bio-oil coming from hydrothermal liquefaction and Soxhlet extraction of microalgae, and the gasoline cut obtained after distillation of the full bio-oil. Results in on-line RPLC x SFC-qTOF were particularly interesting, with very good peak shapes and high reproducibility. Moreover, the high degree of orthogonality for microalgae bio-oils of RPLC and SFC was highlighted by the very large occupation of the separation space. Isomeric profiles of compound families could be obtained in RPLC x SFC-qTOF and many isomers not separated in SFC alone were separated in RPLC and vice versa, thus showing the complementarity of the two chromatographic techniques.