Bottas, who leads five-times world champion Hamilton by a point in the standings, narrowly pipped the Briton to pole position for Formula One's 1,000th world championship race.
Ferrari, who had the quickest car two weeks ago in Bahrain, could not match Mercedes around the 5.4-km circuit with Sebastian Vettel and Charles Leclerc forced to settle for third and fourth.
Mercedes team boss Toto Wolff said the plan would be to "run and hide" in Sunday's race.
"I think the start is going to be certainly very exciting, I hope not too much," added the Austrian. "And then if you have a decent start, it’s about trying to survive these first few laps."
Ferrari’s dominance in Bahrain, where Leclerc took pole and was on course for an easy maiden win until engine trouble denied the Monegasque with 10 laps to go, was due in large part to their speed on the straights.
With the Shanghai track’s main straight more than a kilometre long, Ferrari could use their speed to rocket past their silver rivals at the start.
Wolff said Mercedes had worked on being faster through the corners.
He recognised that the team would have to be careful about their two drivers racing each other too hard early on to avoid opening themselves up to attack from behind.
"I think this is a very important discussion to have," added Wolff. "We have had that discussion since Monza 2014.
"That was the race after Spa," he added, referring to the 2014 Belgian Grand Prix in which an early collision between now-retired 2016 world champion Nico Rosberg and Hamilton cost the team an easy win. "So it’s part of our normal procedure.”
Wolff said the start had the potential to be interesting, with his two drivers, the Ferraris and a frustrated Max Verstappen all hoping to make up spaces.
"It’s certainly, I wouldn’t say explosive, but it’s an interesting constellation," said Wolff.
(Editing by Alan Baldwin and Clare Fallon)
