This study analyzes the impact mechanism of new quality productive forces on the resilience of the pharmaceutical manufacturing industry chain, promoting high-quality development of the pharmaceutical manufacturing industry. Based on panel data from 31 provinces from 2018 to 2023, the article establishes a comprehensive evaluation index system for new quality productive forces and pharmaceutical manufacturing industry chain resilience, and conducts empirical research using multiple econometric models. Baseline regression results indicate that new quality productive forces have a strong positive promoting effect on pharmaceutical manufacturing industry chain resilience. Mediation effect tests show that new quality productive forces indirectly enhance pharmaceutical manufacturing industry chain resilience by promoting industrial structure upgrading. Heterogeneity analysis reveals that compared with the western and eastern regions, the central region demonstrates a more pronounced effect of new quality productive forces in promoting pharmaceutical manufacturing industry chain resilience enhancement. The threshold effect model verifies that there exists a single threshold effect of new quality productive forces between new quality productive forces and pharmaceutical manufacturing industry chain resilience. Based on the empirical research results, it is recommended to strengthen science and technology innovation drivers, promote industrial structure optimization and upgrading, implement regionally differentiated development strategies, and optimize threshold-crossing paths, in order to enhance the overall resilience level of China’s pharmaceutical manufacturing industry chain.