Thomas, the 2018 Tour winner, had targeted the time trial as a late-season goal after finishing runner-up at this year’s Tour to Ineos team-mate Egan Bernal.
The 33-year-old will still represent Britain in next Sunday’s road race at the championships.
“I’ve tried to get back into shape after my post-tour break, but unfortunately I don’t feel in good enough shape to perform to my best,” Thomas said in a statement released by British Cycling on Saturday.
“So the decision was made with my coach and Matt Brammeier at British Cycling to skip the TT and commit to the team for the road race.”
British Cycling’s performance director Stephen Park backed Thomas’ decision and said John Archibald would take his place.
“While it’s a shame that Geraint is withdrawing from the time trial, we understand and support his decision,” he said. “Geraint will still represent Great Britain in the road race where he will be a real asset to the team.”