In 2017, Taiwan’s government proposed reforms to the Indigenous Specialized Criminal Court (ISC) within its criminal court system (court system). Situated within the contemporary theoretical framework of transitional justice, this article explores the theoretical significance of these reforms and examines their actual state of implementation. Firstly, the article points out that the court system has led to structural injustices like the erasure of culture and socio-economic disadvantages for indigenous peoples, highlighting the limitations of the conventional transitional justice model in addressing these injustices. As a response, the ISC reform adopts strategies that differ from the conventional model. The article then attempts to develop an enhanced transitional justice model that includes structural injustices within its scope and explains the ISC reform initiatives and their inherent transitional justice significance. Finally, by evaluating the implementation status of the ISC reform, the article elucidates its theoretical implications and the feedback it offers to contemporary theoretical debates.