The German World Cup winning striker struck twice against the Spaniards to give Bayern fans a huge lift following the departure of midfielder Bastian Schweinsteiger to Manchester United last Monday.
Mueller opened the scoring on 16 minutes, collecting the ball from captain Philipp Lahm before twisting his body and smashing home with his right foot on the edge of the penalty area.
Valencia equalised ten minutes later when Rodrigo nodded in from close range, but it was a another link up between Lahm and Mueller which put the Germans ahead again.
Lahm found Mueller in space after the powerful striker cleverly moved away from his markers. Mueller then stroked home with his left foot to reclaim the lead for the Bundesliga side moments before half time.
Spaniard Thiago Alcantara extended Bayern’s lead before Valencia could get into their stride following the break, sliding onto a low cross on 54 minutes.
Polish striker Robert Lewandowski then put the game out of reach with a curling shot mid-way through the half.
Bayern’s victory at the Bird’s Nest — the main venue for the 2008 Olympic Games — was their first match of a three game tour of China.
They will meet Italian side Internazionale in the commercial hub of Shanghai on Tuesday before heading into a clash with Chinese champions Guangzhou Evergrande in the country’s south on Thursday.
The team arrived in China without a handful of stars, including French winger Franck Ribery, Dutch midfielder Arjen Robben, and Brazilian defender Dante, who are all injured.
Schweinsteiger, who had been a constant in the success of Bayern over recent years, moved to United for a reported £14m (19.47m euros, $21.72m). – Agence France-Presse