Thon also represented Germany at the UEFA Euro 1988 played on home soil, scoring through a rare header against Denmark (2–0 group stage win), and playing all the matches and minutes for the eventual semifinalists. Due to either injuries or run-ins with national team manager Berti Vogts, the player missed the 1994 World Cup and the Euro 1992 and 1996 tournaments, ending his 14-year international career with 52 caps (three goals). His last international match came against Iran in Germany's last group stage game during the 1998 FIFA World Cup.