With the increasing interflow between Taiwan and China, and in conforming to the changing trends in global security perspectives, the security relations across the Taiwan Straits are being transformed from traditional national security to the non-traditional human security. The significance of Cross-Strait health security is gradually being emphasized due to the spreading of infectious diseases (such as the SARS outbreak in 2003) through millions of human contacts and tremendous economic activities. Based on the epidemic situations, infection patterns, and levels of influence, this study analyzes the most influential infectious diseases, namely, enterovirus,avian influenza A (H5N1), HIV/AIDS, and tuberculosis, which mostly affect the security of Cross-Strait health. The way to tackle the health security threats resulting from these infectious diseases is also discussed and needed proposals are drawn up. The cooperation mechanism is recommended with a view to the following: to enhance the communication through the platform of international organizations, such as the World Health Organization (WHO); to strengthen bilateral talks across the Straits; and to expand the second track dialogue.