Flood disasters in Malaysia pose recurring challenges to humanitarian operations, necessitating stronger internal capabilities within responding organizations. While prior studies have acknowledged the individual roles of human resource management (HRM) and logistics coordination in disaster response, there is limited empirical research examining their combined impact on humanitarian operations performance (HOP), particularly within Southeast Asian contexts. This study addresses that gap by evaluating the dual and synergistic effects of HRM and logistics coordination on HOP among humanitarian organizations operating in Malaysia. The present study employed a quantitative approach using the partial least squares structural equation modeling, which was selected for its strength in modeling latent variables and managing complex, non-normally distributed data. A structured questionnaire was distributed to personnel involved in disaster response across the Malaysian Civil Defence Force (APM) and non-governmental organizations (NGOs) in Malaysia, resulting in 29.7% valid responses. The respondents, identified through the National Disaster Management Agency database, had substantial field experience in flood-related humanitarian missions. Findings revealed that both HRM and logistics coordination significantly and positively influence HOP, with HRM having a greater effect. This underscores the importance of integrating strategic human capital development and synchronized logistics systems in disaster response planning. The study’s novelty lies in its empirical validation of these internal mechanisms within a unified model specific to flood disasters in Malaysia. The results provide practical insights for policymakers and humanitarian leaders, while also contributing to sustainable development goals 9, 16, and 17 by promoting resilient infrastructure, effective institutions, and inter-organizational collaboration.