The charges include: use of a weapon of mass destruction resulting in death; bombing of a place of public use resulting in death, malicious destruction of property resulting in death, conspiracy, and use of a firearm during and in relation to a violent crime, federal prosecutors said in a statement.
Dzhokhar, 19, is one of two ethnic Chechen brothers accused of carrying out the twin blasts near the Boston Marathon finish line on April 15.
A fourth victim, a university police officer, died in a gunfight with the pair four days later as authorities raced to capture them.
Seventeen of the charges carry the possibility of the death penalty. The others carry the possibility of as much as life in prison.
Dzhokhar aka "Jahar Tsarni" is a US citizen from Cambridge, Massachusetts.
The indictment alleged that Dzhokhar and his 26-year-old brother Tsarnaev Tamerlan conspired to use improvised explosive devices (IEDs) against people, property and places of public use.
Specifically, the indictment alleges that on April 15, 2013, during the 117th running of the Boston Marathon, Dzhokhar and his brother placed IEDs among the crowds of spectators who were cheering the runners on Boylston Street towards the marathon finish line.
After placing the IEDs among the crowd, the indictment alleges, Dzhokhar and his brother detonated the bombs seconds apart, killing three people, maiming and injuring many more, and forcing a premature end to the marathon.
The indictment alleges that the IEDs were constructed from pressure cookers, explosive powder, shrapnel, adhesives and other items, and were designed to shred skin, shatter bone and cause extreme pain and suffering, as well as death.
Tamerlan was killed after a shootout with police on April 19 in Watertown. Dzhokhar was arrested after he was found hiding in the boat later that day.