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The USB ports on the board are not working, the version of my board is using a flex cable connected to the DE-10 USB port and the Ironclad board.
I confirm the micro-USB port on the DE-10 is fine by connecting the DE-10 and my PC with a cable, I can see the DE-10 SD card content.
Any idea what cause the USB ports not work?
It sounds like it is almost certainly the micro USB flex cable. Carefully remove the DE10-Nano, re-seat all the flex cables and visually inspect the micro USB connector for damage. Make sure you are inserting it correctly as outlined here.
Failing that I would get in contact with d3fmod, their contact details are on their website.
My board is working fine after flash MiSTer to a SD card. Before that I used the original SD card that comes from DE-10, it seems the Linux is not compatible with the board.
Were you trying to boot from USB? Regardless, I'm pleased to hear you've got things working.