Bio-oils obtained from the pyrolysis of lignocellulosic biomass are highly complex matrices with tens of thousands of organic compounds covering a wide polarity and mass range. Their upgrading into greener fuel or value-added chemicals requires an in-depth knowledge of their molecular composition prior and after valorization treatment, which can be obtained by different analytical techniques. Here, flash chromatography was employed as an efficient way to fractionate a bio-oil vacuum residue into four distinct fractions. This process was repeatable at both gravimetric and chromatographic levels and provided information about the weight contribution of each fraction to bio-oil composition. Achieved fractions were then characterized by ultra-high-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and nuclear magnetic resonance spectroscopy. These two techniques ensured the good repeatability of bio-oil fractionation at the molecular level and also highlighted molecular specificities of each fraction. Thus, flash chromatography provided quantitative information that was complementary to FT-ICR MS results. It also simplifies the bio-oil compositional analysis, making it possible to detect more compounds. Eventually, this fractionation process can also be used to target fraction or compounds of interest for bio-oil upgrading.