is it worth visiting Chengdu Panda Breeding and Research Center in the late afternoon?

I think it's too late to visit the pandas, you'd better go in the morning or early afternoon.

It depends on when you come to Chengdu. The giant pandas will go back their air-conditioner room around 9:30am in hot summer. And maybe you can not see them outside. Instead, you may see them inside. As I know, there are at least 7 places you can see the pandas inside the room, including No.2House for giant pandas, No.14 Encosure, Moon Nursery House asnd so on. But the weather in Chengdu is not stable in summer. Therefore, you must check the weather first before you come here.