The 20-year-old from Northern Ireland made a 15-foot birdie putt at the Road Hole 17th, then drove the green at the famous 357-yard closing hole and two-putted from 40 feet.
He was at 11-under 133 with Richie Ramsay of Scotland and Michael Hoey of Northern Ireland. Ramsay, who only got in the tournament when fourth-ranked Paul Casey pulled out last week, shot 66, also on the Old Course.
Hoey had a 66 at Carnoustie.
McIlroy said he got a confidence boost from his father, Gerry'his pro-am partner here'after a setback on the 16th.
I had just three-putted the 16th for my only bogey of the day, McIlroy said, and going to the 17th tee Dad said to me, ‘You've finished 3-3 here before, so why don't you do it again.'
The field of 168 golfers plays one round on each of the three courses being used for this championship'the other is Kingsbarns'before the final round on the Old Course on Sunday.
Another Scot, Alistair Forsyth, shot 64 at Kingsbarns to share second place, one shot back, with Simon Dyson , Ross McGowan and Mikko Ilonen . Ilonen shot 64 and Dyson 66 on the Old Course, while McGowan had a 68 at Kingsbarns.
It was a day for good golf, but I couldn't finish anything off, Harrington said. I just didn't hole any putts.
First-round leader Thomas Bjorn dropped to a 74 at Carnoustie, 10 shots off his first round, for a share of 20th place.
All 168 pros play with an amateur partner for three rounds, and McIlroy is clearly enjoying his father's company.
I've played really well the last couple of months, and especially with my dad with me this week I can freewheel. I think that's why I started so well, McIlroy said.
More significantly, he will almost certainly take over the lead in the lucrative Race to Dubai. He is currently third behind Martin Kaymer and Casey, who are both absent with injuries.
McIlroy's round also included an eagle-3 at the long fifth, where his 5-wood second shot from 255 yards stopped 12 feet from the hole.