Bad weather over the winter has taken its toll on several of the greens at Quail Hollow, with two of them - the eighth and 10th - dug up and relaid just a week before the start of the Wells Fargo Championship.
All 18 bentgrass greens will be replaced with Bermuda grass when the tournament is over, but McIlroy is taking a pragmatic and light-hearted approach to the situation.
"The greens are the best on tour usually, it's just unfortunate that they are not quite up to the standard they usually are," the world number two told a pre-tournament press conference.
"It's no big deal, the rest of the golf course is in phenomenal shape and it's going to be the same for everyone. The best player at the end of the week is still going to win.
"If you start missing putts I guess you have to accept it. I don't mind because I'm not a guy that relies on my putting per se, so it will eliminate quite a lot of the field and I don't mind that at all."
As for the rest of his game, McIlroy believes it is in better shape than might be thought after a tie for 25th on his last appearance at the Masters last month.
"I feel good," added the Northern Irishman, who won five times around the world last year but has struggled to rediscover such form in 2013.
"I had two sevens on the back nine on Saturday (at Augusta) but I played solid on Sunday, shot 69 and at least came away with some positives.
"I've done some good work with Michael (Bannon, his coach) in Florida last week, the game feels in good shape so hopefully I can continue that this week."
McIlroy found himself making headlines despite not playing last week when R&A chief executive Peter Dawson said that there may be a rule which would take the difficult decision over who to represent at the 2016 Olympics out of McIlroy's hands.
The 23-year-old would be eligible for selection by either Great Britain or Ireland, but had said he may opt out instead for fear of upsetting people with his choice.
Speaking last year, McIlroy said: "Whatever decision I make, whether that's play for Ireland, play for Britain, not play at all maybe just because I don't want to upset too many people...."
Asked if not playing was a genuine possibility, he added: "For sure it's definitely an option. I've got three options; I either play for one side or the other or I don't play."
Dawson said the fact that McIlroy had played for Ireland in the World Cup may mean he would have to stick with Ireland at the Olympics, but McIlroy said: "I think it's Rule 41 but I still have a choice. They can't take it away from me.
"If you change country or don't play for that country for three years you still have a choice. I've not played for anyone since the World Cup in 2011, the Olympics would be five years so I still have a choice.
"The more it's talked about it's just going to get blown up. I would rather not talk about it until the time I have to decide what to do."