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Four bio-oils obtained from the hydrothermal liquefaction (at 280 °C for 0 min) of untreated and pretreated cypresses were subjected to several types of chemical analyses to compare their structural features and chemical constituents. Pretreatments were carried out with alkali at 90 °C for 0.5, 1, and 2 h. The bio-oils were further divided into water-soluble oil, diethyl ether-soluble oil, and diethyl ether-insoluble oil fractions. Alkaline pretreatment had a significant effect on the contents of different components in the bio-oils. The diethyl ether-insoluble oil fraction was made up of intermediate-sized macromolecular fragments of lignin decomposed during the hydrothermal liquefaction process. The G6 resonance, β-5, β-β’, and β-O-4’ peaks (which were present in the spectra of milled-wood lignin) almost disappeared from the spectra of the diethyl ether-insoluble oil fractions obtained via hydrothermal liquefaction of pretreated and untreated cypresses. At the same time, the intensities of the peaks corresponding to methoxy groups, G2, and G5 resonances were reduced. Long-duration alkaline pretreatment created a strong, highly water-soluble oil fraction with a wide molecular weight distribution.