Brexit will not only change the UK and the EU’s economic cooperative relationship，but also reshape their security cooperative relationship，in particular their cooperative relationship in terms of counter-terrorism. This article is set to explore how Brexit will reshape the UK’s relations with the EU’s current counter-terrorism cooperation mechanisms，and in what way the counter-terrorism cooperation between the two sides will be possibly changed in the future. The UK has already established a close relationship with the EU in combating terrorism，as demonstrated by its deep and broad participation in the current EU counter-terrorism mechanisms，including data sharing mechanisms，criminal justice tools and criminal justice institutions. There remains uncertainty about the future UK-EU cooperative relationship in terms of counter-terrorism. Nevertheless，given their increasingly common interests in anti-terrorism，the UK and the EU will be highly likely to form a special and close cooperative relationship in dealing with common threat from terrorism in the future.