Here is a link which shows how to replace the top motherboard in your controller. This is to show you how you gain access to the micro USB port.
The micro USB port is mounted on this motherboard. You would either have to re-solder it onto the motherboard if it was only pulled loose from the board and was not damaged or if it was damaged, remove it and replace it with a new one
Here is an Ifixit guide on how to replace the top motherboard.
Xbox One ワイヤレスコントローラの上部基板の交換
To replace the connector you would need the following:
1. tools to open the Xbox One controller (see guide)
2. replacement female micro USB connector (available from Ebay, Amazon etc) if the original is damaged. You cannot repair them.
3. soldering iron and tools
4. skills in soldering components on pcb