The charges were announced Monday during a 45-minute hearing in Centennial, Colo.
Holmes also was charged with 166 counts of attempted murder, one count of possession of explosive devices and one count that is a sentence enhancer in the July 20 massacre at the Century Aurora 16 movie theater complex during a midnight screening of the latest Batman movie, "The Dark Knight Rises," CNN reported.
Prosecutors said they essentially filed double the number of charges because it was a premeditated, planned attack and because Holmes showed extreme indifference, CNN said.
Immediately after Holmes' first court appearance last week, prosecutors said they wanted to leave open the possibility of more charges being filed.
Unlike last week's hearing, cameras were not allowed in Monday's proceeding, which many survivors and families of victims attended.
One survivor who attended the hearing told CNN survivors of the theater shooting wanted to show Holmes how strong and united they are.
Holmes, still sporting his red-and-yellow dyed hair, reportedly said one word during the hearing. After conferring with his attorneys about whether to seek a delay for the preliminary hearing, the defendant told the court, "Yes."
Meanwhile, weekend donations brought the Aurora Victim Relief Fund to $3.1 million, Community First Foundation online giving manager Dana Rinderknecht told The Denver Post.
A pregnant woman whose 6-year-old daughter was killed in the Aurora shooting, and was herself seriously wounded in it, suffered a miscarriage, her family said Sunday.
The attack was the deadliest mass shooting in Colorado since the 1999 Columbine High School attack in which 12 students and a teacher were killed and 24 others were wounded.
First-degree, or premeditated, murder of multiple victims can be punishable by death in Colorado.