According to a statement from the US Attorney's Office, Central District of California, Alsheikh concealed his employment at the prison and denied persecuting anyone in his US visa and citizenship applications.
US officials say Alsheikh personally inflicted "severe physical and mental pain and suffering on political and other prisoners" in his role under ousted President Bashar al-Assad.
He allegedly ordered detainees to the "Punishment Wing" in the prison, where they would be beaten while suspended from the ceiling and subject to a device which would cause "excruciating pain", sometimes resulting in fractured spines.
"Almost 20 years ago, the defendant was accused of torturing prisoners in Syria and, today, we are one step closer to holding him accountable for those heinous crimes", the Special Agent in Charge of the HSI Los Angeles Field office, Eddy Wang, said in a statement.
If convicted, Alsheikh faces up to 20 years in prison for the conspiracy to commit torture charge; up to 20 years for each of the three torture charges; and up to 10 years for each of the two immigration fraud charges.
In a statement to the Associated Press, Alsheikh's lawyer says he "vehemently denies these politically motivated and false accusations".