Omar Uresti, Richard Barcelo, Michael Flynn and Joel Kribel share third at 3-under-par 69.
'I don't think there will be a lot of low scores all week,' said Thatcher. 'This golf course is incredibly difficult. I had a day where I did a lot of things right. I got a lot of really good distances and made a lot of good swings.'
Thatcher found trouble early on the Bayonet Course with a bogey at the par-4 third. However, the dropped shot proved to be Thatcher's only blemish on Thursday.
The 25-year-old birdied the following hole to get back to even-par and picked up three straight birdies starting at the par-3 sixth to make the turn at minus-3.
'To tell you the truth, the first 12 holes I didn't mishit a golf shot,' said Thatcher. 'The longest birdie putt I made was from 12 feet. I was striking the ball really well. It was one of those stretches all of us get on at one time or another when everything is going right and I was able to ride it.'
Thatcher continued his fine play on the inward half with a birdie at the par-5 10th. He added a birdie at the 11th to make it two in a row.
The Auburn University grad capped off his round with a 15-foot birdie at the last to enter the clubhouse with the outright lead.
'I've never played in a U.S. Open but from what I can tell, this would be comparable to that. It's got to be the Buy.Com Tour's U.S. Open,' said Thatcher. 'I've heard a lot of guys mention it this week. That's the style of golf you have to play out here because the fairways are so tight, the rough is tall and thick and the greens are very firm.'
Thatcher, a rookie on the Buy.Com Tour this season, posted a top-10 finish at the third event of the year but has since struggled. Thatcher has missed the cut in each of his last six starts.
Cliff Kresge, who is seeking his third victory of the season, collected four birdies and two bogeys to finish alone in seventh at 2-under-par 70. Kresge is looking to follow in the footsteps of Chad Campbell, who made this tournament his third title of 2001 en route to an exemption on the PGA Tour.
Charles Warren, who won the Charity Pro-Am at The Cliffs in April, was one shot further back at 1-under-par 71. Warren was joined by John Elliott, Barry Cheesman, Todd Fanning, Todd Bailey, Dave Schreyer and Mike Brisky in a tie for eighth.
Arron Oberholser, another two-time winner on tour this season, finished in a group at even-par 72.
Full-field scores from the Bank of America Monterey Peninsula Classic