Pudong Airport to Hongqiao Railway Station after midnight?

You can take the night airport bus after the mid night, which is operated from 23:00 - 05:00 with an interval of 45 minutes. The bus ticket fare is CNY 34 and it takes about 2 hours.

As I know, no regular trains are available to Nantong now, and only bullet trains are possible. The earliest departure is at 6:01 and you'd better book it in advance.