As ISIS clashes with al Qaeda for prominence in the global jihadist movement, Morell said Friday on "CBS This Morning" that it takes on "one of the most important terrorist groups in the world" and with 10,000 fighters, one of the largest.
Boko Haram benefits from the association with ISIS.
"They're now playing with the big boys. They're going to get more money. They're going to get more recruits," said Morell, a former CIA deputy and acting director.
In a recent audio message, ISIS spokesman Abu Mohammed al-Adnani announced the terror group embraced Boko Haram. He gave ISIS' blessings to Boko Haram and called on Muslims to immigrate to West Africa if they are unable to reach ISIS-held land in Iraq and Syria.
Al-Adnani also said, "We are setting our sights on Paris before Rome and Granada...but that will be after we blacken your lives, and blow up your White House, Big Ben, and Eiffel Tower, Allah willing."
While Morell doesn't believe the alliance makes ISIS more dangerous, the relationship does have an effect on the West African terror group.
"Boko Haram, for a long time, has focused primarily on local Nigerian targets. This alliance could now get them to focus more on the West, and that's the danger here," Morell said.
Despite al-Adnani's message, Morell said, "they're not a threat to us yet."
"I think if they become one, then it becomes a different story, but I think we cross that bridge when we come to it," Morell said. "Right now we stay focused on the head of the snake and that's ISIS in Iraq."
In February, ISIS released a digital handbook offering tips to successfully travel to the terror group's capital in Raqqa, Syria. It offers advice on what to pack and who to contact. Morell described it as a "travel guide."
"What I found interesting about the handbook is the colloquial English that's used in it," Morell said. "It's clearly written by a Westerner, a Brit, an American."
Whether the guide should be of concern, Morell said "I think there are many, many ways to get to Syria and it's very easy to get to Syria. I don't think you really need a handbook," Morell said.