The Northern Irishman, who is competing in the event for the first time since 2009, carded eight birdies and just one bogey on his way to seven under at Royal Aberdeen.
Sweden's Kristoffer Broberg had set the record at 65 earlier in the day but it lasted just two hours as former world number one McIlroy topped that effort.
The 25-year-old coped superbly with the windy conditions, and even managed to reach the green in one at the par-four 13th.
"Everything was pretty much on," McIlroy told the European Tour's official website. "I controlled my ball flight really well which is the key to me playing well in these conditions and on these courses.
"I've been working the last 10 days on keeping the ball down, hitting easy shots and taking spin off it and I went out there today and really trusted what I practiced."
Brogerb's card was unblemished and he was thrilled with his opening round, adding: "I played really, really well. I hit very good shots and a lot of close ones, so this helps a bit."
Argentina's Ricardo Gonzalez had been in contention to beat McIlroy's score, as an eagle at the par-five 12th left him eight under for the tournament.
However, he dropped shots at 13 and 16 to be left in a tie for second with Brogerb, one stroke ahead of Michael Hoey.
Luke Donald is one of four players on four under, while reigning champion Phil Mickelson - who is gunning to become the first man to defend the trophy - is a further shot back.
Frenchman Francois Calmels had a moment to savour with a hole-in-one at the eighth, while Englishman Tom Lewis also bagged an ace at the penultimate hole, the 25th in tournament history.
The competition carries extra importance, as three players - who are not already exempt - that finish in the top 10 will qualify for The Open Championship at Royal Liverpool, with Mickelson aiming to defend the major he won 12 months ago.