The charges against the trio -- an architect and a technician, both 26, and a 42-year-old trader -- come amid concerns over the group's growing influence in Southeast Asia.
The men were arrested on September 25 at Kuala Lumpur international airport as they were about to board a flight to Syria's neighbour Turkey.
They are accused of supporting a "terrorist group", said prosecutor Shukor Abu Bakar. The maximum penalty for the charge is life imprisonment.
Malaysian authorities arrested 14 people earlier this month for suspected links to the extremist group, including a government engineer and others who sought to recruit Malaysians and to arrange for their travel to Syria.
In total, around three dozen have been detained in the country this year over IS-related activities, but only some have been charged with some others still under investigation.
At least 40 Malaysians are believed to have left for Syria.