Wales' Carlin, 26, who won 400m and 800m freestyle silver medals at the 2016 Rio Olympics, has been affected by illness and injury this year.
England's double Commonwealth silver medallist Willmott, 24, has not fully recovered from an ongoing knee injury.
The event will be held in Budapest, Hungary between 14-30 July.
"Rio was such a high for me but this year I have struggled with niggles and injury and in hindsight my body needed a break to recharge," Carlin said.
"I'm still training steadily in Bath and will be looking to build whereby come September I'll be raring to go for next season, driving towards Tokyo 2020."
British Swimming head coach Bill Furniss said: "Both swimmers are a loss to the team but we respect their decisions which we believe will have a positive impact on their long-term futures.
