The 23-year-old German, who was the European Tour's rookie of the year in 2007, shot the best round for the second straight day to total 13-under 131.
Henrik Stenson of Sweden, who was runner-up in the inaugural event in 2006, was second after a shooting 70.
England's Steve Webster was 7 under through 11 holes before shooting 68 for a share of third place at 138 with Gonzalo Fernandez-Castano of Spain (68).
Kaymer was again accurate with his driver, hitting 16 greens in regulation, while he needed only 26 putts to record eight birdies, with one bogey.
'I hit the ball great ... maybe not as good as yesterday, but my putting was very good out there,' Kaymer said. 'I have had better two consecutive rounds, but that was the EPD Tour and it was a totally different golf course. This is a golf course on the European Tour and that makes it a big difference.'
Kaymer had rounds of 59 and 62 in a satellite European Professional Development Tour in Germany just days after turning pro in 2005.
'I am just going to take it hole-by-hole and stick to my game plan,' Kaymer said. 'I am not even thinking of a victory yet. Henrik is obviously a really, really good player and he can easily play 7 or 8 under on this course, like I did today.'
Adam Scott, the highest ranked player in the field at No. 8, overcame a terrible front nine of 41 to come home in 3 under to shoot 74 and be 11 shots off the pace at 2-under 142.
British Open champion Padraig Harrington added a second consecutive 72 and was tied for 42nd.
The cut was at 1 over with defending champion Paul Casey among those to miss it.