Maritime security cooperation is a strategic approach engaged by the Malaysian government that involves a bilateral agreement with the United States (US), including the various agencies and organizations. The involvement with maritime security is due to the emergence of serious Non-Traditional Security (NTS) threats over the Malaysian waterways (Straits of Malacca, the South China Sea and the Sulu Sea in Eastern Sabah). The bilateral security cooperation aims to overcome the Malaysian government’s gaps and limitations to govern its waterways. A qualitative method was used in this research to explain the implication of the US-Malaysia maritime security cooperation towards Malaysia’s national security, specifically in the maritime domain, from 2010 until 2021. This research has two objectives, namely; 1) to investigate maritime security issues and challenges and 2) to identify the importance of the US Malaysia maritime security cooperation. The national security concept was used in this research to support the maritime security collaboration between the US and Malaysia. This study found that Malaysia faces challenges and constraints from obsolescence, lack of maritime assets, and weaknesses in enforcing maritime laws, mainly dealing with increasing traditional and non-traditional security threats. Second, Malaysia can reduce the gap in the governance of maritime routes through bilateral security cooperation with the US. This study concluded that Malaysia can maintain the peace and security of its maritime routes and improve and strengthen bilateral cooperation with the US through various stages, especially economic recovery in the post-pandemic era of COVID-19. Bilateral maritime security cooperation is a crucial factor that will shape future global maritime governance to ensure national security stability.