Pharmaceutical process residues (PPRs) are the byproducts from pharmaceutical industry that is popular and developed rapidly nowadays, involving two typical categories: Chinese herb residues (CHRs) and antibiotic fermentation residues (AFRs). Due to the dual attributes of renewable resource and hazardous waste of PPRs, to realize their safe and value-added utilization is of great significance to the society, the industry and the enterprise for environment protection and resource saving. In this study, focusing on the most accessible thermo-chemical conversion strategies, the research progress on the characteristics and influential factors, the evolution mechanisms of elements or components, and the properties of PPR-derived biofuels (solid, liquid and gas) are reviewed. Results demonstrate that the defective components (high moisture, rich nitrogen and abundant oxygen) are big obstacles to the conversion of PPRs into desirable biofuels, impeding their clean and efficient thermal utilization. On one hand, some pretreatments like dehydration and torrefaction can acquire enhanced performance of solid biofuels by the capabilities of upgrading and denitrogenating PPRs focusing on the evolution regulation of moisture, carbon and nitrogen fractions, while the enhancement effect is still limited together with the proper disposal of secondary byproducts. On the other hand, thermo-chemical conversion (pyrolysis, gasification or hydrothermal liquefaction) strategies on PPRs can produce favorable gaseous or liquid biofuels with higher energy density, nevertheless, the quality or the yield of resultant biofuels (pyrolytic gas, gasified gas, biogas and bio-oil) would be all inhibited in varying degrees due to the evolution and conversion of unfavorable/useless components (such as nitrogen, oxygen and ash) in PPRs. To fulfill stringent emission standards and high-efficient thermal utilization, more efforts should be made to develop satisfying strategies on the valorization of PPRs into biofuels in a more eco-friendly and profitable way. Furthermore, by comparing the properties and uses of various PPR-derived biofuels, hydrothermal integrated with subsequent thermo-chemical approaches seems to be a preferred option when focusing on the clean and efficient valorization of PPRs.