The Irish border problem, a contested issue in the Brexit process, constitutes to be an unsolved question for the UK and the EU in the post-Brexit era. The UK and the EU signed the Protocol on Ireland and Northern Ireland as part of the Withdrawal Agreement. Nevertheless, the operation of the Ireland and Northern Ireland Protocol has triggered political wrestling amongst the EU, UK central government, Northern Ireland, and Ireland. Since the Brexit referendum, differentiated disintegration as a theoretical approach has attracted much attention in the study of European integration, and the UK's withdrawal has been regarded as the latest and most significant case study. This paper aims to explore the Irish border problem after Brexit, with a special focus on the implementation and controversy of the Northern Ireland Protocol, by employing the theoretical approach of differentiated disintegration. This paper is, therefore, designed with the dual purpose of conducting the empirical case study of the development and challenge of the Irish border problem in the post-Brexit era, and of examining the theoretical validity of differentiated disintegration against the case study of the Irish border problem.