Waitrose plans to take over the 6,230 sq ft former Woolworths in September and open by October, following a multi-million pound refurbishment.
But Thornton, who owns a well-established Budgens store just a few doors down, said he was confident he could compete.
"At the end of the day, we have fought off competition from Marks & Spencer and Tesco and we can do it again," he said.
His store, which he said attracted "celebrities, journalists and lots of influential people", is known for its trailblazing ideas such as introducing a charge for plastic carrier bags, placing bins by checkouts so customers can dump unwanted packaging, and stocking products from other local retailers. Thornton also owns a second Budgens store in Belsize Park and together the stores turned over £16.9m in the year to September 2008.
However, other independent retailers would suffer, he predicted. "A number of residents are quite concerned and don't think it's a good move because the character of the area is made by the number of independents we have."
Waitrose insisted the store would "provide a wider choice of shopping services for the local community" and create 60 jobs.
"We have found a location that will allow us to attract shoppers to the high street and trade successfully," said Waitrose director of development, Nigel Keen. "Our objective is always to make a long-lasting positive contribution to any area we serve. It is in our best interest to ensure Crouch End is an attractive place for visitors and we look forward to having the opportunity to work alongside our fellow traders."
It will be Waitrose's third convenience store in the country, after it launched its first in Nottingham in December and its second in Bristol in March.