The pair, suspected of helping Moroccan gunman Ayoub El Khazzani, were charged with "participation in the activities of a terrorist group", Belgian prosecutors said in a statement.
They were among four men held on Monday as part of the probe into the August 2015 attack, which could have been a bloodbath but for the actions of quick-thinking passengers -- including two off-duty US servicemen -- who overpowered the heavily-armed Khazzani as he opened fire.
The prosecutor's office identified the pair who were charged as Mohamed B. and Youssef S. They are both Belgian.
Thalys attacker Khazzani, a Moroccan who fought for IS in Syria, has told investigators he was acting on the orders of Abdelhamid Abaaoud, one of the organisers of the Paris attacks, whom he met in the war-torn Middle Eastern country.
Prosecutors said "no explosives nor weapons were found" during Monday's raids, one of which was in the gritty Brussels district of Molenbeek. The district gained notoriety as a hotbed of international jihadists after the attacks in the French and Belgian capitals.
The other two men arrested on Monday were released after "thorough questioning", Belgian prosecutors said.