• The overall innovation efficiency of pharmaceutical manufacturing enterprises in the Beijing-Tianjin-Hebei region is not effective, with significant regional differences.
• The establishment period, market competitiveness, and financial constraints significantly impact innovation efficiency, while government subsidies show no significant positive effect.
• The three-stage DEA model effectively separates environmental factors and random errors, providing a more accurate efficiency evaluation.
• Policy recommendations include establishing an innovative drug risk warning mechanism and innovation incentive and risk-sharing mechanisms to enhance innovation efficiency.
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