The highly-rated midfielder has been heavily linked with a switch to the reigning Bundesliga champions for some time, while the likes of Arsenal, Barcelona and Liverpool have also been reported as admirers
Schalke spotted his potential early when acquiring the 22-year-old from Bochum, but face losing him as a free agent at the end of his contract next summer.
Former Germany international Thon believes “a minor miracle” is required to prevent that from happening, with Goretzka destined to be heading for the Allianz Arena.
He told Goal: “He has a lot of self-confidence at the moment.
“Nevertheless, I believe that all contracts with Bayern are sewn up. At least that is my impression.
“The fact that no-one is talking about this topic at the moment is very suspicious.
“Regarding him staying at Schalke, I am anything but optimistic. Schalke would need a minor miracle.”
Thon represented Schalke and Bayern during his playing days, with a spell in Bavaria sandwiched by two in Gelsenkirchen.
While the World Cup winner believes that Goretzka could soon tread a similar path, he feels that an extended stay in current surrounds for a man who starred at the 2017 Confederations Cup would be no bad thing.
He added: “Goretzka's current sporting situation would be a good reason for him to extend his contract.
“He is in good form, he is scoring goals and has taken on a leadership role. He is the undisputed man in the midfield and deputy captain as well.”
Goretzka opened his goal account for 2017-18 in his most recent outing for Schalke against Werder Bremen, with his 83rd-minute effort proving to be the winner.
He managed seven in all competitions last season, before going on to net three times at the Confederations Cup as Germany tasted more international success a year out from starting the defence of their World Cup crown.