As an important part of human enhancement technology, brain-computer interface technology has a wide range of application scenarios in the medical field, especially in the treatment and rehabilitation of neurological diseases, which has significant advantages over traditional therapies. At the same time, the application of brain-computer interface technology in the medical field brings ethical challenges. First, privacy issues and the loss of human autonomy. Second, it triggers the dilemma of responsibility attribution of relevant subjects and laws. Third, it causes potential mental health effects on users. Fourth, the technical fairness caused by brain-computer interface is controversial. To deal with the ethical problems arising from brain-computer interface at the medical level, the first is to construct ethical principles to solve the privacy risks of brain-computer interface technology, the second is to clarify the attribution of relevant responsibilities through technical governance and non-technical governance, the third is to guide all parties to improve the cognitive level of brain-computer interface technology, and the fourth is to solve the dispute of technical fairness through technical optimization. In the medical application of brain-computer interface technology, the goal of technological goodness has always been established.