Implantable brain-computer interfaces (BCIs) have potentially important clinical applications due to the high spatial resolution and signal-to-noise ratio of electrodes that are closer to or implanted in the cerebral cortex. However, the surgery and electrodes of implantable BCIs carry safety risks of brain tissue damage, and their medical applications face ethical challenges, with little literature to date systematically considering ethical norms for the medical applications of implantable BCIs. In order to promote the clinical translation of this type of BCI, we considered the ethics of practice for the medical application of implantable BCIs, including: reducing the risk of brain tissue damage from implantable BCI surgery and electrodes, providing patients with customized and personalized implantable BCI treatments, ensuring multidisciplinary collaboration in the clinical application of implantable BCIs, and the responsible use of implantable BCIs, among others. It is expected that this article will provide thoughts and references for the research and development of ethics of the medical application of implantable BCI.