Ebden broke the Cypriot's serve three times to win through to his second tour-level semi-final of the year with the 6-3 6-2 result.
With the US Open just a month away, the World No.18 will have to overcome the recurrence of an issue that has plagued him since Queen's past year.
Isner improved to 29-4 in the event, winning his second match after a 6-hour, 36-minute loss - with a 26-25 fifth set - to Kevin Anderson in the Wimbledon semifinals. "I was happy to get through in three sets".
"I knew he was going to be tough here, because he lives here", Ebden said.More news: 'Erratic' winds, dry conditions fuel deadly California fires
World No.9 Isner is 8-1 in the Atlanta semi-finals, with the lone loss coming to Andy Roddick in 2012. He had the home crowd on his side.
Kyrgios leads their head-to-head meetings 3-0 against Harrison, the Australian prevailed in 2018 Brisbane, 2017 Madrid and 2016 Tokyo.
"Now, I'm playing in my backyard and he beat me in his backyard".
That helped set up the second straight Isner-Harrison Atlanta final with Isner triumphing a year ago.
"I always feel comfortable playing here. the court suits my game style", he said on Friday after a comfortable win over American Noah Rubin.
The 23-year-old also landed himself in hot water during the Queen's Club Championships last month, when he was captured on live television simulating a sex act during a change of ends. "But we'll see what happens".