After being ill over the past week, he has been replaced by Courtney Tulloch.
Whitlock, 23, became the first British man to win World Championship gold, on the pommel horse, in 2015.
He said on Twitter: "Really gutted to withdraw from the Europeans, I have to look at the bigger picture. Massive good luck to the team."
A British Gymnastics statement said "it was felt better to give him time to fully recover with the Olympic Games in mind".
Men's head national coach Eddie van Hoof added: "The withdrawal of Max is unfortunate and we will look at some tactical reshuffling of the team order, but it is testament to the depth of the programme that we can call upon Courtney to step up.
"Courtney has great experience and was a rings finalist in the Nanning World Championship in 2014."
World champion Max Whitlock has been withdrawn from Great Britain's artistic gymnastics European Championships squad because of a virus.