"It's a culture clash," Cramer said on "Squawk on the Street." "It's like naming a guy from the Army to run the Air Force."
Chipotle has cultivated an image obsessed with using high-quality ingredients, something Taco Bell is not known for, Cramer said. The choice of Niccol is ironic, Cramer said, because he's probably "the most opposite guy you can find."
Chipotle railed against Taco Bell for years, the host of CNBC's "Mad Money" continued. "They never mentioned Taco Bell by name. They don't like the race to the bottom. They don't' like the dollar. They don't like to get you in on convenience," he said.
A spokesperson for Chipotle responded with this comment:
"From the beginning of the search for a new CEO, we noted that we wanted an experienced leader with a passion for driving excellence across every aspect of our business, and that was a top consideration for the search committee throughout the process. We are confident we found that in Brian Niccol, who himself noted: "I have tremendous respect for the Chipotle brand and its powerful purpose." We're confident with where we landed through this process."
Chipotle announced its decision late Tuesday to tap Niccol as the replacement for CEO Steve Ells. The announcement sent the stock soaring. CMG was up nearly 15 percent on Wednesday, putting it on track for its biggest daily gain since October 2013, when it rose 16.1 percent. Even with the stock rise, Chipotle is 42 percent off of its 52-week high of $499 on May 16, 2017.
Chipotle is hoping the fast-food veteran Niccol can enhance the consumer experience at its restaurants, which have seen sluggish growth and battles with food-safety problems.
Niccol was president of Taco Bell from 2013 to 2014 before becoming CEO in 2015. He's credited with repositioning Taco Bell as a lifestyle brand and launching the chain's breakfast offerings.
While criticizing Chipotle's move, Cramer did say, "This is a man who knows how to get food fast to you cheaply." He's known for efficiency and known for "getting the job done."
In Tuesday's press release about the change, Ells said: "Niccol's expertise in digital technologies, restaurant operations and branding make him."
While giving up the CEO job, Ells will remain chairman.
—CNBC's Sarah Whitten contributed to this report.