McIlroy, 19, finished at 13-under 200 at Crans-sur-Sierre Golf Club.
Juan Abbate (69), Alejandro Canizares (69), Christian Cevaer (65), Julien Clement (67), Robert Dinwiddie (64) and Jean-Francois Lucquin (69) are knotted in second place at 9-under 204.
McIlroy can make history if he can hold on Sunday. He would become the third-youngest winner on the European Tour.
'I'm in control of my golf game,' said McIlroy. 'Hopefully, I can just do the same things tomorrow. As long as I do that tomorrow, I should have a good chance.'
McIlroy flew out of the gate. He knocked his second to 4 feet at the par-5 opening hole and converted the eagle putt. McIlroy drained a 9-footer for birdie at the third, but drove it out of bounds at the fourth en route to a bogey.
McIlroy atoned for the error at four with a 6-footer for birdie at the fifth. Two holes later, McIlroy holed a 10-foot birdie putt to reach 12 under for the championship.
After a pair of pars at eight and nine, things went downhill a bit for McIlroy. At the 10th, he hit a strong approach to 15 feet, but ran his birdie putt 3 feet past the cup. McIlroy missed that putt for a bogey, then hit into a bunker at the 11th. He saved par from the sand, but three-putted for a bogey from inside 20 feet at No. 12.
His lead dropped to a single stroke, but McIlroy responded. His tee ball at the par-3 13th spun back to 3 feet and McIlroy kicked in the birdie putt to get back to 11 under.
At the par-5 15th, McIlroy reached the green in two. His eagle putt narrowly missed the hole, but he tapped in for another birdie to pad his lead to three shots.
McIlroy hit a sensational approach to 3 feet to set up birdie at the 17th. At the last, McIlory's second stopped 15 feet from the hole. His putt hit the edge of the hole, but popped out.
He tapped in for par and will take a four-shot lead into the final round in his quest for history.
'I think it could've even been better,' acknowledged McIlroy. 'I let a couple of short putts go there at 10 and 12, but I came back really well and finished the round off nicely.
'If I can go out and hit good golf shots and hit good putts, the rest will take care of itself. Hopefully I will have a good night's sleep and come out fresh tomorrow.'