There are lots of places in Shanghai, so here is just a brief list:
Bus: Shanghai Bus Station-上海客运总站, Shanghai South Bus Station -上海客运南站
Train: Shanghai Railway Station-上海火车站, Shanghai South Railway Station-上海火车南站

For the subway, you could see all of the stations at https://www.travelchinaguide.com/cityguides/shanghai/transportation/subway.htm

The Shanghai Railway Station has four express trains to Beijing everyday. The journey is about 10hours and costs about 450RMB per person~