If TUSB1310 can work simultaneously on USB2.0 and USB3.0?

Sorry,"TUSB1330 PHY" in drawing  should be "TUSB1310 PHY"

This is not a valid USB3 situation.  Only the upstream port of a USB3 hub can have a simultaneous USB2 and USB3 connection.  A USB device must connect at either USB3 or USB2 speed upon enumeration.  So a USB device with the TUSB1310 in it can only connect at either USB2 or USB3 speed at one time.

USB3.0 HUB include USB3.0 and USB2.0HUB,

 the result is not is the same, TUSB1310 can not work on the USB2.0 and USB3.0 at one time.

I don't understand what you are trying to do.  Are you trying to implement a USB hub or a USB device?

As the following drawing:

Can TUSB1310  handle the USB2 & USB3 at the same time,and  exchange data with FPGA?

Yes, the 1310 can do simultaneous transactions, but unless you are implementing a hub or host this is not a valid USB device.

Thanks very much!