Higher Education Evaluation & Accreditation Council of Taiwan (HEEACT) was established in 2005 and began to accredit 76 four-year comprehensive universities and colleges in Taiwan in 2006. Commissioned officially with a dual mission, HEEACT has been encouraged to conduct various ranking research projects, including global and national ones starting in 2007. One of the HEEACT's most influential rankings is "Performance Ranking of Scientific Papers for World Universities." Given the fact that more and more national accrediting bodies are developing ranking systems, these dual roles like in the HEEACT case have led to many discussions and raised severe criticism in the quality assurance community due to their different aims and approaches. Therefore, the purposes of the paper are to provide an understanding of the functions of varying quality assessment tools in higher education, to analyze their impact on Taiwan higher education and to examine the conflicting roles of HEEACT while conducting both accreditation and rankings over the institutions that have been granted the two major national Research and Teaching Excellence Programs.