Jetson Nano PCIe

As per the product design guidelines PCIe can be used in x4 configuration only, but my carrier board requirement is 2 different x1 PCIe device (2 different endpoint). Can it be possible to use a 1:2 PCIe clock buffer and implementing 2 different x1 PCIe device using Jetson Nano module.

No, only one interface up to 4 lanes for use on the carrier board.

You MUST use a PCIe bridge in order to get multiple downstream PCIe connections.

This would be suitable for your project: