The Pakistani, Majid Shoukat Khan, has been held at the US military's prison at Guantanamo since 2006.
The Pentagon accuses him of cooperating in terror plots against the United States and Indonesia under the supervision of alleged September 11 mastermind Khalid Sheikh Mohammed. He also is accused of trying to assassinate Pakistan's former president Pervaiz Musharraf.
Khan is scheduled to be arraigned at Guantanamo within 30 days.
The 31-year-old lived in the United States from 1996 to 2002 before being detained in his native Pakistan in 2003. He is one of 14 high-value prisoners held under conditions of maximum security at the controversial US military-run prison.
The charges say Khan and Mohammed – also being held in Guantanamo – conspired to blow up underground tanks at US gas stations and assassinate Pakistan's then-president Musharraf in a suicide bombing inside a mosque.
Military prosecutors also accuse him of delivering $50,000 in al Qaeda funds to a southeast Asia-based affiliate in Bangkok.
The funds later were given to another radical group that used them to carry out the bombing of a Jakarta hotel in 2003, killing 11 people and wounding at least 81 others, according to the US military.
Khan has been formally charged with "conspiracy, murder and attempted murder in violation of the law of war, providing material support for terrorism and spying," a Pentagon statement said.
He faces a maximum penalty of life imprisonment.
Military Commissions rules and procedures now require the chief trial judge of the military commissions' Trial Judiciary to assign a military judge to the case.
Khan is the seventh Guantanamo detainee to be formally charged since US President Barack Obama assumed office in January 2009 and the second to be referred to a military tribunal after Saudi Abd al-Rahim al-Nashiri, the alleged mastermind of the attack on the USS Cole in October 2000.
The five other detainees, including Mohammed, have been charged with planning the September 11, 2001 attacks on New York and Washington but still are awaiting trial by a military tribunal.
In a brief statement, Khan's lawyers said they are "reviewing the charges and will represent Majid throughout this process. Majid is doing well considering these challenging circumstances."
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Majid Shoukat Khan and other kidnapped men held hostage at that illegal, immoral camp are indeed victims of crime. Kidnapping is a crime under those countries where civility is in the Law. Kidnapping is not a crime under the "Laws of the Jungle". This camp is a testimony that "Laws of the Jungle". are being enforced upon the people of the USA by some men of the most evil men of the Jungle. Such men most unfortunately rule over the most decent and hardworking people of the USA. Why? There is no democracy in the USA and anywhere else in the world. If there was democracy in the USA, then decent men would be ruling over the USA.