Most Rev Justin Welby said I.S. was a "once in a millennium" threat to the survival of Christians in the Middle East.
The extremist group has taken over large parts of Iraq and Syria, forcing tens of thousands of Christians to flee.
In some towns its militants threatened believers with death if they didn't pay a tax or leave.
Archbishop Justin compared the militants with the Mongol hordes who conquered parts of the Middle East in the 13th century, killing entire populations.
The archbishop was speaking to ITV News and recalled a meeting with Christian leaders from the Middle East.
"They had flown here for this meeting from situations of the utmost horror; indescribable horror," he said.
"We spent two hours listening to their stories. The memorable comment was 'this is the worst threat we've faced since the Mongol invasion of 1259'.
"This is an extraordinary once in a millennium threat."