The application value of Brain-Computer Interface (BCI) and human-machine integration technology in the fields of UAV control and countermeasure equipment operation is explored, the problems faced by these technologies are analyzed, and targeted solutions are proposed to promote their rational application in the development of the low-altitude economy and security protection. By analyzing the role of BCI technology in improving UAV control efficiency and enhancing the accuracy of countermeasure equipment operation, and combining the new application scenarios that BCI technology shapes for the low-altitude economy and the new form of low-altitude security protection it creates, the problems faced by these technologies are sorted out, such as inherent defects of human-machine integration technology, information security risks, and their impacts on low-altitude security, and corresponding countermeasures are further put forward. BCI technology plays a significant role in the fields of UAV control and countermeasure equipment operation: it can improve UAV control efficiency and enhance the accuracy of countermeasure equipment operation. Based on BCI and human-machine integration technology, new application scenarios for the low-altitude economy have been shaped, and a new form of low-altitude security protection has been created.