Thermodynamic modeling studies on biomass conversion processes, where the Shell hydrothermal upgrading of biomass (HTU) process was adopted as an example, have been carried out. These include the establishment of the method for the characterization of the biocrude and selection of estimation methods for the physical properties of the biomass and biocrude. Models have been selected and modified for the description of the phase equilibria (VLE and VLLE) involved in the process. Estimation methods have been developed for the exergy of biomass and biocrude in order to perform an exergy analysis of the process. Our research has provided a complete thermodynamic tool for the HTU process development and design, which is also applicable to other biomass conversion processes.