Thatcher stands at 15-under 127, matching Jon Mills' 2005 record at one of the developmental tour's biggest events -- and one of its most notorious shootouts.
He opened with a 64 in the first round.
'It is hard to follow up a good round with a great round. So to post an 8-under after a 7-under is obviously tremendously satisfying,' said Thatcher, already a winner this season at the Peek'n Peak Classic.
Scott Sterling had a 3-under 68 and was alone in second place at 13-under 129.
Chris Thompson followed his 60 in the first round with a 71 on Friday to slip from first place overnight into a tie for third place with Miguel Carballo (63) and Michael Walton (64).
That trio stood at 11-under 131, with Chez Reavie (65) and Chris Anderson (66) sitting another shot further back at 132.
They are all looking up at Thatcher, who hasn't posted a bogey in his last 32 holes.
Beginning on the back nine Friday, Thatcher made four birdies in his first six holes, then later birdied four of six again to finish the round with a two- shot lead.
'Hopefully I can do the same thing the next couple of days,' said Thatcher.
But with players going so low at Champions Run -- the cut line was a season- low 5-under -- even another 63 won't guarantee Thatcher a hold on the lead. Position changes drastically day-to-day at this tournament.
Just ask Daniel Summerhays.
The first amateur to win on the Nationwide Tour when he claimed the Children's Hospital Invitational two weeks ago, Summerhays turned pro before this tournament and opened with a 71 in the first round.
Friday, he fired a 7-under 64 and climbed all the way from a tie for 110th place into a tie for 25th place, safely making the cut in his first start as a professional.
The start of Friday's round was pushed back one hour after overnight storms dumped 2.4 inches of rain on the course.