The world number four had opened with a 72 on Thursday. His halfway total of one over par was well short of the cut, on a day when first-round leaders Benjamin Hebert from France and American Daniel Im stayed ahead of the field. Each posted a 67 to end on 13 under par.
Spain's Jon Rahm also shot 67 to stay one shot behind, on 12 under. A cluster of others, including Japan's Hideto Matsuyama, remain in touch with the leaders.
For McIlroy, it was another disappointing tournament to add to many more in an injury-affected season.
"I felt like I was battling well, two under through 13 and with another par five coming up, and to bogey the sixth took the wind out of my sails," said the Ulsterman, who showed his frustration by slamming his driver to the ground after a poor drive at the 16th.
"My short game, in general, it's just silly mistakes," he said. "I'm just not being very efficient with my scoring and that's why I'm making it difficult for myself. Just need to tidy up the short game a little bit; I feel like the long game is there."
McIlroy will compete in next week's Scottish Open before heading down to Royal Birkdale for the British Open.
"Obviously, I might have a few commitments here this weekend, but I need to practice," he said. "I need to get sharp and get ready for next week and ultimately for The Open in a couple week's time."
Also missing the weekend action are Ireland's Darren Clarke and Paul McGinley, who finished on eight over.
(Reporting by Neil Robinson, editing by Larry King)
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