I will reach pudong at 5:30 in morning. can you suggest which is best route to yiwu city?

There are direct coaches to Yiwu from the airport. However, the first departure is scheduled at 9:00, and the duration is about 4.5 hours. So, you are advised to travel by train.

Take metro line 2 to Hongqiao Railway Station in about 1.5 hours. High speed trains to Yiwu are scheduled from 6:30 to 20:33 there, and they have 27 departures each day. It takes about 1.5 hours to reach Yiwu.