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As a critical defense mechanism against COVID-19, the national public health emergency response system (PHERS) with high resilience enables effective identification, absorption, and resistance of epidemic crises. This resilience is essential for safeguarding public health and rapidly restoring social stability. However, existing studies primarily focus on single-aspect strategies in specific countries, lacking a systematic understanding of how resilience strategies influence PHERS resilience outcomes. Therefore, this study aims to establish evidence-based and configurational resilience strategies to improve the effectiveness of PHERS in responding to epidemic threats. This study proposes a theoretical framework to characterize resilience strategies and resilience outcomes for PHERS. The fuzzy-set qualitative comparative analysis (fsQCA) method is applied to analyze data from 40 countries during the COVID-19 crisis. The findings reveal three configuration paths to enhance robustness and three paths to enhance rapidity. These results emphasize the importance of the synergistic implementation of containment and closures, travel control, public personal protection, and early virus detection in improving PHERS resilience. This study provides a structured approach to understanding PHERS resilience by identifying key configuration paths that enhance robustness and rapidity. The results offer actionable insights for designing resilient PHERS to better respond to future epidemics.