There is a conflict between judicial independence and democratic accountability. In Taiwan, this problem is particularly serious in Taiwan’s prosecutorial system. In 2007, the Ministry of Justice transferred and appointed chief prosecutors. Nine members of the Prosecutorial Council who were elected by prosecutors boycotted these personnel cases. In order to understand the root of the problem, this paper first discusses how reform-minded judges used the Judicial Council to reform the judiciary, while reform-minded prosecutors used the Prosecutorial Council to reform the prosecutorial system. However, both of them ignored the importance of democratic accountability because of the poor quality of Taiwan’s democracy. This paper offers a proposal in which some members of the Judicial Council are politically appointed while some are elected by judges and prosecutors to seek a balance between judicial independence and democratic accountability.