The next Commonwealth Games take place on the Gold Coast of Australia during April 2018, which is right when Thomas will be racing in Europe.
Speaking to BBC Wales, 30-year-old Thomas said that fellow Welsh Sky riders Luke Rowe and Owain Doull would also miss the Commonwealth Games for the same reason.
"Unfortunately I think the three of us will be out of it," said Thomas.
"Where they fall in April is the wrong time for us. Luke and Owain will still have the cobblestone classics in Belgium, which will be their main target.
"At the end of the day, Team Sky pay us to race bikes for them and we've got to do what they say."
Thomas won the men's road race at the 2014 Games in Glasgow, after a solo attack that was very nearly scuppered by a late puncture. However, Thomas had built up enough of an advantage to keep eventual second and third placed riders Jack Bauer (New Zealand) and Scott Thwaites (England) at bay.
The 2014 Games took place in August, ideally positioned after the Tour de France.
"If it was similar to Glasgow and after the Tour, then it might have been doable. Especially with it being down in Australia it's not like you can fly over to France and be in and out over a weekend, it's a big old trip down there."
Despite having to miss the 2018 Games, Thomas says that the 2014 road race win and time trial bronze medal for his home nation of Wales remains one of his career highlights.
"To come away with two medals and win the road race was unbelievable, and something I'll always remember and I'll always consider to be one of my biggest victories," said Thomas.
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