The federation is the latest to leave SportAccord, an organisation representing close to 100 Olympic and non-Olympic sports federations and organisers of multi-sports games, after SportAccord President Marius Vizer's scathing attack on the IOC last month.
"We have aimed to create a clear identity for the sport of boxing in the past 8 years of my presidency," said AIBA chief Ching-Kuo Wu in a statement.
"Boxing is a noble art and a traditional Olympic sport and we feel that the participation in the World Combat Games challenges this identity among boxing fans."
The decision is a further blow to Vizer, who emerged as a self-styled reformer of international sport when he took over the SportAccord presidency two years ago.
He instantly clashed with the IOC, proposing the creation of the United World Championships, a possible competitor to the Olympics, a project that has not materialised
Vizer, who also heads the international judo federation, said last month the IOC was dated and in need of serious reform and it should stop interfering in the autonomy of other sports bodies.
In a heads-on collision Vizer accused the IOC of blocking the creation of other events and deciding which sports could compete where, in an unprecedented attack launched in front of the entire Olympic leadership at the SportAccord convention in Sochi.
"It is with much regret that we suspend our membership with SportAccord with immediate effect. AIBA’s work is based on the Olympic values and it is the values of integrity and respect that we must protect first and foremost," Wu said.
AIBA had been a member of SportAccord since 1967 and boxing had been part of the SportAccord World Combat Games in Saint Petersburg in 2013 and Beijing in 2010.
It joins several other federations, including athletics (IAAF) to withdraw from the organisation.
The 2017 World Combat Games, which include sports such as aikido, fencing, judo, karate, kickboxing, sambo, weightlifting and wrestling among other, will be held in Lima, Peru.
After AIBA's withdrawal only five of the 16 World Combat Games sports are Olympic sports.