The 46-year-old, who spent six years with die Roten between two spells at Schalke, suggested that the 22-time German champion would be facing a weaker Arsenal side than of previous times.
"Arsenal had to sell their top stars in recent years," the former coach of semiprofessional side VfB Huls told Goal.com. "Now they have got some Bundesliga stars, but they do not meet the highest standards, although [Per] Mertesacker and [Lukas] Podolski are doing quite well at the moment. Podolski plays one great match after another.
"I saw Schalke playing against Arsenal and the Gunners reached this round having big difficulties. That is why Bayern will not have any problems. Jupp Heynckes can go into these matches calmly."
The retired midfielder also explored Borussia Dortmund's chances of reaching the Champions League quarterfinals.
"[Shakhtar] Donetsk are unknown, they do not have any big names in their squad. But that is also dangerous," said Thon. "I saw Dortmund. This team is in outstanding form. They are dominant. The attacking trio of Gotze, Reus, Lewandowski - these are fantastic players.
"That is why Dortmund are absolute favorites for this match. The second leg is at home, that is another advantage. Donetsk are not a weak team, but they are constantly eliminated early."
The 52-capped international added that he did not believe all German teams would have an easy route to the quarterfinals, however.
"I remember well playing against Trabzonspor in the UEFA Cup in the 1996-1997 season," he said. "They were a very strong opponent, and so Galatasaray will be in this round for Schalke.
"You can not compare those two teams, but the Turkish fans will support their team to death. It is an even game, but the second leg at home could be an advantage for Schalke."