The high contents of nitrogen-containing organic compounds in biocrude obtained from hydrothermal liquefaction of microalgae are one of the most concerned issues on the applications and environment. In the project, Chlorella sp. and Spirulina sp. were selected as raw materials to investigate the influence of different reaction conditions (i.e., reaction temperature, residence time, solid loading rate) on the distribution of nitrogen in the oil phase and aqueous phase. Three main forms of nitrogen-containing organic compounds including nitrogen-heterocyclic compounds, amide, and amine were detected in biocrudes. The contents of nitrogen-heterocyclic compounds decreased with temperature while amide kept increasing. The effect of residence time on the components of nitrogen-containing organic compounds was similar with that of temperature. However, the influence of solid loading rate was insignificant. Moreover, it was also found that the differences of amino acids in the protein components in the two microalgae might affect the nitrogen distribution in products. For example, nitrogen in basic amino acids of Spirulina sp. preferred to go into the aqueous phase comparing with the nitrogen in neutral amino acids of Chlorella sp. In summary, a brief reaction map was proposed to describe the nitrogen pathway during microalgae hydrothermal liquefaction.