As I know, there is only one train departing from Yangzhou at 12:20 to Shanghai, taking about 5.5 hours on the way. The destination is at Shanghai South Railway Station, where you could take the shuttle bus Line 7 to Pudong Airport directly.

On the other hand, there are many coaches from Yangzhou to Shanghai everyday, taking about 4 hours on the way. When you arrive in downtown Shanghai, you could take the subway Line 2 or Maglev train to Pudong Airport as well.