David Coleman Headley conducted extensive surveillance of targets in Mumbai for more than two years preceding the attack on India's largest city that killed about 170 people, the DoJ said in a statement.
Mr Headley, 49, was charged with six counts of conspiracy to bomb public places in India, to murder and maim persons in India and Denmark, to provide material support to foreign terrorist plots, and to provide material support to Pakistani-based terror organization Lashkar-e-Taiba.
He was also charged on six counts of aiding and abetting the murder of US citizens in India.
Mr Headley is the first American to be charged.
In October, Mr Headley and Tahawwur Hussain Rana, 48, were alleged to have been involved in a plot they codenamed the “Mickey Mouse Project” to attack facilities and employees of Morgenavisen Jyllands-Posten, a Danish newspaper that offended many Muslims with its Mohammed cartoons.