I'm travelling from Beijing to HK via Xian, Chongqing, Guilin, Shanghai in this Sept.

The average temperature in Beijing, Xian, and Chongqing maybe 65-85F in that month. The rest cities should be a little hotter of 75-85F.
Generally speaking, there will have large temperature difference between day and night during that period of time. Thus you are advised to prepare some jackets and overcoats.