It is the sixth stint in a bid to fly around the world that began in Abu Dhabi, UAE on 9 March.
Solar Impulse was only supposed to stay a few hours in Chongqing after arriving from Myanmar (Burma), but poor weather grounded the plane for three weeks.
The team is now confident conditions will remain fair for the Nanjing leg.
Getting to the east of the country would set up the project for its greatest challenge yet - a five-day, five-night crossing to Hawaii.
The latest leg saw Solar Impulse leave the runway at Chongqing International Airport at just after 06:00 local time, Tuesday (22:00 GMT, Monday). Project chairman, Bertrand Piccard, is again at the controls of the single-seater aircraft.
He is taking it in turns with CEO Andre Borschberg. But as the engineer in the partnership, Borschberg wants to do the Hawaii leg, so Piccard has elected to do both Chinese stages. He brought the plane in from Mandalay, Myanmar, to Chongqing, and is now flying the 1,200km to Nanjing as well. It should take him about 17 hours.
Once in Nanjing, the team will stay put for at least 10 days, carefully checking over the aircraft and running through a training programme ahead of the first Pacific leg.
"I think 10 days is the time we need to get ready. Then we need to wait for a good weather window," explained mission director Raymond Clerc.
"That could be three days; we could have to wait three weeks - because this leg is really the most important and is very complex. To go towards Hawaii could last five days and five nights."
Nanjing is about 200km from the coast, very close to Shanghai. The first Pacific leg would cover a distance of more than 8,000km.
Article by Jonathan Amos
(Source: bbc.com)