Does baiyun airport shuttle bus line 1 stop at Guangzhou South Train station?

No, it doesn't. Line 1 leads to the Civil Aviation Ticket Office near the Main Railway Station. And no a shuttle bus is set for the South Railway Station. To get there, you may use subway. Take line 3 to Jiahewanggang and transfer to line 2 to reach. In this way, it takes almost 70min and costs CNY9. The train leaves from airport from 06:10 to 23:00 by the way.