The American fired a seven-under par 64 to finish on a 72-hole tournament record of 28-under 256 at TPC Deere Run in Silvis, Illinois.
Thompson, ranked 70th in the world, broke the old mark of 27-under set by American Michael Kim in 2018.
Thompson followed his sizzling start with back-to-back birdies at nine and 10 then answered his lone bogey at 12 with a birdie at 14 and parred his way into the clubhouse.
"I just tried to stay present all day," Thompson said. "When that putt finally went in, just a big sigh of relief."
Taiwan's C.T. Pan, American Michael Thorbjornsen and US amateur Luke Clanton shared second on 260 with Americans Ben Griffin, who shot 62, and Carson Young another stroke adrift.
"A lot of confidence seeing the ball roll in today. It was nice," Griffin said. "It was a really good round."
In his 63rd PGA start, Thompson took his first trophy after a runner-up finish last week in Detroit, another in May at Myrtle Beach and one last year in the California desert.
"It's great," Thompson said. "I've been working hard this year. It was OK for a while then I kind of got going this past month. Played well last week and just tried to keep it rolling this week and I was able to get the win."
Thompson and Pan, the top two not already qualified for the British Open, earned a berth into the showdown at Royal Troon in two weeks. Pan took a spot by having a higher ranking than Clanton or Thorbjornsen.
"Qualifying for the Open was just an added incentive into this," said Thompson. "The goal was to win the golf tournament after getting here this week and I got off to a great start and was able to finish it off."
'Trophy House' winner
Thompson's rental house this week is the same one used in their winning year by 2022 John Deere champion J.T. Poston and 2023 John Deere champion Sepp Straka of Austria. Thompson even has the same bedroom Straka used last year.
It might be only luck, but Thompson isn't planning on giving up his spot in the "Trophy House" even though it comes with an expensive tradition.
"Definitely not," Thompson said. "I think I have to pay for the whole house now, which is unfortunate, but I'll gladly write the check for that."
Clanton didn't qualify for Troon but he did become the first amateur since Billy Joe Patton in 1958 to finish in the top-10 in PGA Tour events in back-to-back weeks.
Thompson, who began the day with a two-stroke lead, made a birdie putt from just inside 45 feet at the first hole and a tap-in birdie at the par-5 second.
He made birdie putts from just inside 14 feet at the fourth, just inside 30 feet at the fifth and just inside 13 feet at the sixth.
Thompson birdied the ninth from just beyond six feet and the par-5 10th and after a bogey at 12 had a tap-in birdie at 14.
