Hanson had a 14-under 130 total on The Masters Course at Lake Malaren.
The top-ranked McIlroy had seven birdies a 65.
Hanson matched his lowest score on the tour.
"The biggest difference in my career compared to earlier times, is that I am playing better in the bigger events like the majors and the World Golf Championships that has helped my confidence quite a lot," said Hanson, the KLM Open winner this year for his fifth European Tour title.
"Also, being a part of the Ryder Cup team, and being high up the world rankings, you feel you maybe belong a bit more competing alongside the best players."
Hanson bogeyed his opening hole but quickly rebounded to enjoy a run of nine birdies in a 13-hole span.
"It's amazing how many good rounds can start with a bogey," he said. "The key to my good two rounds is that I've birdied all the par 5s which can help dramatically around this place."
McIlroy had three straight birdies on Nos. 13-15.
"When I did need to make a par here or there, I was able to save those, and I'm in a great position going into the weekend," McIlroy said.
McIlroy hasn't won a regular European Tour event since the Hong Kong Open last year. Of his four wins this year, all in the United States, only the PGA Championship counted toward the European Tour money list. Yet McIlroy leads the list, and was four shots clear of Rose, his nearest rival in the Race to Dubai.
"It looks quite routine at the moment," McIlroy said. "The more you put yourself in this position, the more comfortable you become with it. I like the fact that most weeks I tee it up, I can get myself in contention. "This is just another one of those weeks, and I'll try and continue that for as long as I can."
Sweden's Robert Karlsson was three strokes back after a 64.
Karlsson is winless since the 2010 Dubai World Championship.
However, the Monaco-based Swede admitted is concerned about retaining his U.S. PGA Tour card. He is 158th on the PGA money list and needs to be 125th by the end of the season, which is why he has entered the tour finale on Nov. 8-11 at Lake Buena Vista, Fla. He wants to avoid Q-school, which clashes with the European finale in Dubai, but doesn't think he can get around it.
"At the end of the day I am in a very fortunate position as I have another year of exemption for the European Tour," he said. "There are a lot of players in a lot worse situation than I am, so I am not complaining. I haven't had a good year and you have to accept the consequences. So a good result this week, and what with the huge world ranking points on offer, will help with the confidence to put together some decent rounds."