Morrison, a team mate of test cricketers-to-be Alastair Cook, Tim Bresnan and Ravi Bopara when they were all teenagers, raced into a four-shot lead on 12-under 132.
Six birdies and a second eagle three in a row at the 18th gave him an eight-under 64.
Sharing second place on 136 were world number two and defending champion Luke Donald (68) and his fellow Briton David Drysdale (70). Ireland's Peter Lawrie (71) was a further stroke adrift alongside Spain's Alvaro Quiros (70).
The leading quintet, who teed off early, were lucky with the draw but Britain's McIlroy was among the late starters who had to contend with swirling winds that made good scoring almost impossible in the afternoon.
Former cricketing all-rounder Morrison, 27, bowled over the huge crowds who gathered on another sun-kissed day at the European Tour's flagship event.
"This is my third year on the tour and that's definitely one of the best rounds I've ever had," the 2010 Madeira Islands Open champion told reporters at Wentworth on the outskirts of London.
"It was also probably one of the easiest, or at least it felt easy. I wish golf was like that every day but it's not."
Morrison focused on cricket as a youth when he played alongside Cook, Bresnan and Bopara.
"Cricket was my life but not now," he said. "I started playing golf when I was 16, went from an 18 handicap to scratch in 10 months and haven't really looked back.
"Playing golf is better than standing in the field all day at cricket, I can tell you that."
A former opening batsman and spin bowler, Morrison hung up his cricket gear after hitting a century for Surrey's under-17 team.
"I wasn't enjoying it," he said. "I still follow the people I played with because I love watching sport.
"I also used to play county hockey too. I was playing all three sports at one time."
Morrison, who hails from nearby Chertsey, said he had lost touch with Cook, Bresnan and Bopara.
"I haven't spoken to any of them for years," he said. "I'm not sure but I probably wouldn't have made it at cricket.
"You could always see that those three were far better than anyone else at 16, 17."
Morrison, who finished 61st and 57th in the order of merit in his first two seasons on the European Tour, said his golf had come on in leaps and bounds in the last two months.
"My coach and I have been working really hard and my game has turned full circle," he said. "I used to be short off the tee and a bit crooked but I had a great short game.
"Now I'm 15, 20 yards longer than I have ever been and it's helping around this course because it's pretty long at 7,302 yards."
Nothing seemed to help McIlroy as he added an out-of-sorts 79 to his opening 74.
"I think I might have taken my eye off the ball a little bit," he said, referring to his second successive missed cut following his poor show at the Players Championship in Florida two weeks ago.
"Maybe I'm not practising as hard as I might have. I didn't hit many fairways on the back nine today and from there it's very hard to get close to the hole.
"Pretty much everything went wrong the last couple of days," added McIlroy after avoiding an 80 with a last-hole birdie.
The young Northern Irishman seemed at odds with himself all day and a rush of dropped strokes around the turn effectively ended his involvement in the tournament that carries a prize fund of 4.5 million euros.
Ryder Cup team mates Graeme McDowell, Padraig Harrington, Peter Hanson and Ross Fisher, last week's World Match Play champion Nicolas Colsaerts and British Open winner Darren Clarke also missed the cut.
World number three Lee Westwood made it through to the weekend by the skin of his teeth after a 75 for 145, one over.