While the milestone development of brain-computer interfaces (BCI) has brought a series of benefits to society, it has also exposed a range of ethical issues. By sorting out the relevant research on BCI conducted by domestic scholars, the research results were discussed at three levels, including subjectivity, epistemology, and axiology. In terms of subjectivity, there was a controversy over the concept of “subjectivity” of BCI, raising the problem of subject responsibility; in epistemology, there were doubts about the new cognitive form brought about by BCI, and the new cognitive approaches exposed potential problems; as for axiology, there was confidence in the macroscopic development of BCI, while concerns about its microscopic individual and social issues were raised. Finally, this paper pointed out that future research needs to be further expanded in research fields and depth, and three governance suggestions were proposed, including improving institutional guarantees and strengthening standardized governance, forming diverse teams and enhancing ethical breakthroughs, and enhancing self-awareness and actively complying with regulations.