Effective and selective biomass processing is crucial in many biorefinery strategies. The selection of a proper processing solvent is important in its process efficiency. Here, the natural deep eutectic solvents (DESs) were fundamentally investigated and applied for different biomass applications. We discussed how the structures of DES constituents played an important role in determining the properties and processibility of the DESs. The unique thermal and physical properties of DESs were discussed with structures and hydrogen bonds between their constituents. The impacts of aldehyde and/or methoxy group(s) of HBDs were investigated with thermal stability, viscosity, and net basicity of lignin-derived DES as well as their fractionation performance. Natural hydrophobic DESs were synthesized to recover polyhydroxybutyrate (PHB) from fermentation cells. The solubility of PHB was tested with the experimental and computational studies. The selected natural DES successfully alternated toxic organic solvents. In short, our recent studies demonstrated the potential of natural DESs as a designer solvent, which can be customized with diverse properties depending on the target applications. Therefore, these green chemicals will be a promising processing solvent in future biorefinery industries.