Public companies must set up internal control system (ICS) according to the Securities and Exchange Act. However, the implementation level of ICS should be assessed by internal auditing department in case of the frauds no matter how the companies have been owned ICS. Fewer researches have focused on investigating the relationship among internal audit quality, internal control deficiencies and earnings management. Hence, the research objects were initial listed companies during 2002 to 2011 from Taiwan Stock Exchange. Survey and secondary data were applied to test the research hypotheses. This study measured and divided internal audit quality into internal audit profession, internal audit independence and budget fit. The empirical results showed that internal audit quality has significant and negative effect on internal control deficiency and earnings management. That means the higher the internal audit quality has, the less occurrence possible of internal control deficiency and earnings management do.