Hydrothermal liquefaction is a promising technology to convert wet biomass into bio-oil. However, post-hydrothermal liquefaction wastewater (PHWW) is also produced during the process. This wastewater contains a high concentration of organic compounds, including phenols and N-heterocyclic compounds which are two main inhibitors for biological treatment. Thus, proper treatment is required. In this work, ozone was used to convert phenols and N-heterocyclic compounds with a dosage range of 0–4.64 mg O3/mL PHWW. After ozone treatment, the phenols were fully converted, and acids were produced. However, N-heterocyclic compounds were found to have a low conversion rate (21.7%). The kinetic analysis for the degradation of phenols and N-heterocyclic compounds showed that the substitute played an important role in determining the priority of ozone reactions. The OH moiety in the ring compounds (phenols and pyridinol) may form hydroxyl radical, which lead to an efficient reaction. A substantial improved biodegradability of PHWW was observed after ozone treatment. The ratio of BOD5/COD was increased by about 32.36%, and reached a maximum of 0.41. The improved biodegradability of PHWW was justified by the conversion of phenols and N-heterocyclic compounds.