Ahmed Muthana identified the man in the 13-minute video, entitled "There is No Life Without Jihad", as his 20-year-old son, Nasser Muthana, from Cardiff.
Speaking to BBC Wales, Ahmed Muthana said seeing the video made him "want to cry" and asked his son "why did you do this?"
"Is he going to kill?" he asked. "He didn't think of the children, the women, elderly people. Someone is driving these kids to do this."
Nasser, who had received four university offers to study medicine, appears in the YouTube video -- dressed in a white turban -- using the name Abu Muthanna al-Yemen and is flanked by five other men, three of whom appear to be British.
His father slammed those who had drawn his son into the conflict, saying they only "send other people's children" into battle.
He accused them of making a problem for whole of the "multicultural" UK, not just the Muslim community.
British police are trying to remove the online film, which was posted by accounts linked to militant group the Islamic State of Iraq and the Levant (ISIL).
The jihadist group is renowned for its ferocity, and is currently fighting against the Syrian regime of Bashar al-Assad and recently took Iraq's second city of Mosul.
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British intelligence believe ISIL has recruited around 400-500 Britons.
Ahmed Muthana told BBC Wales that he was worried his son would "come back to me in a coffin".
He explained that his son had left home in November, and that he believed he had gone to study in Leicester or Shrewsbury.
"I received a phone call saying that he's in Turkey and that's it," he added.
"I don't think that's Nasser talking, it's someone else is teaching him to talk like this because the attitude of Nasser is 100 percent completely different," he said.
The British government on Thursday banned the militant group currently rampaging through northern Iraq, adding it to a list of proscribed organisations along with four other groups linked to the Syrian conflict.
It is now an offence in Britain to belong to or invite support for ISIL and the four other proscribed groups, or even to wear clothing or carry items in public indicating support.
Prime Minister David Cameron is worried that British nationals joining in the fighting in Iraq and Syria pose a threat to Britain's security.
Police have made 65 Syria-related arrests since January 2013, Cameron's office has said, while 14 people had their passports seized in the year to March, "a significant number" of them related to Syria.