Pharmaceutical process residues (PPRs), which are renewable biomass and hazardous biowastes, are by-products of abundant organic matter and high initial moisture from the popular pharmaceutical industry. Chinese herb residues and antibiotic fermentation residues are the two main categories of PPRs, with an annual accumulation of the ten-million-ton scale and rapidly growing in the current post-COVID-19 era. Their conventional disposal (landfill, stacking, and incineration) not only pose risks to the eco-system and human health, but also results in significant resource waste. Over the past few decades, the use of PPRs in energy, environmental, and biochemical applications has received widespread attention. In this review, the preparation, properties, and applications of the resultant bio-based products (mainly biofuels, carbon materials, and bio-fertilizers) are comprehensively discussed. Current challenges and future perspectives on valorizing PPRs in heat supply, environmental protection, energy storage, etc., are systematically summarized. PPR-derived biofuels are the most accessible and easy-to-expand while require cleaner and more efficient strategies. Carbon materials and biofertilizers are two promising options for PPRs, which would be achieved by potential hydrothermal integrated technologies. This review aims to provide an overview of and insights into the efficient disposal and resource utilization of PPRs for relevant researchers.