Zachary Chesser was allegedly held after confessing his links to a terror group believed to be affiliated with al-Quaeda. He admitted that he had attempted to fly to Kenya and Somalia in order to join Al-Shabaab, taking his young son with him on the trip as cover.
Chesser, a convert to Islam, has operated websites and a YouTube channel centred on militant propaganda.
He had previously posted a message online warning Parker and Stone that they could "end up dead" after an episode of South Park depicted the Muslim prophet Muhammed wearing a bear costume.
"It's not a threat, but it really is a likely outcome," he later told Fox News. "They're going to be basically on a list in the back of the minds of a large number of Muslims. It's just the reality."
The new charges against Chesser are in no way related to the South Park controversy.