Hydrothermal liquefaction of microalgae under alkaline and acidic conditions has been widely investigated. However, limited data are available on the mechanism of aqueous phase formation during liquefaction. In the present work, we conducted a detailed characterization of the aqueous phase from hydrothermal liquefaction of Spirulina platensis using acetic acid and potassium hydroxide as the catalyst. GC-MS analysis revealed that a large proportion of nitrogen-based heteroatom compounds and few oxygen-based heterocycle compounds were presented in all the aqueous phase. All the aqueous phase displayed alkalescence and a high level of total organic carbon. Whereas, the addition of potassium hydroxide reduced the total organic carbon and the average molecular weight of the aqueous phase. The conventional liquefaction converted the Spirulina platensis to plenty of water-soluble amides, while these compounds were apt to form acids under both the alkaline and acidic catalysts. Based on the analyses, the general reaction frameworks for the catalytic liquefaction were also proposed.