Abstract: The implementation of cleaner production technologies in the pharmaceutical industry can reduce the generation of pollutants from the source, which is conducive to promoting the healthy and sustainable development of the pharmaceutical industry. In order to correctly select the appropriate cleaner production technologies in the pharmaceutical industry, the evaluation index system of cleaner production technologies in the pharmaceutical industry including technical, economic and environmental indexes was established, and the analytic hierarchy process-fuzzy comprehensive evaluation (AHP-FCE) model was constructed. The evaluation standard of cleaner production technologies in the pharmaceutical industry was determined, and the comprehensive evaluation of four cleaner production technologies in the pharmaceutical industry was carried out based on the AHP-FCE model. The results showed that cephalexin enzymatic synthesis technology was better in technical performance, large-scale preparation technology of immobilized enzyme for antibiotic synthesis was better in economic performance, and penicillin fermentation and emission reduction technology based on medium substitution was better in environmental performance. The comprehensive evaluation results showed that cephalexin enzymatic synthesis technology was the best technology in four cleaner production technologies in pharmaceutical industry.