The charges against the suspects, aged between 26 and 42, were filed at a Sessions Court in Sepang town on the outskirts of Kuala Lumpur, according to deputy public prosecutor Shukor Abu Bakar.
The three could be jailed for up to 15 years if found guilty of attempting to provide support to a terrorist group.
They were arrested on September 25 at the Kuala Lumpur International Airport as they were about to board a flight bound for Turkey.
They were heading for Syria to join IS militants, Shukor said. The three suspects did not enter a plea and Judge Aizatul Akmal Maharani did not grant them bail.
The trial is set to start next month.