my system includes fpga and power supply that are not related and their gnd isn't common
as I described in the attached schem.
I want to switch the power supply 28v output
how should I connect the gnd?
Do you mean you have both a Digital and Analog ground on the same PCB which are connected together at a certain point on the PCB? If that is the case then you would want to connect the switch to the power supply ground as the FPGA ground would be quite noisy.
If the GNDs are completely unrelated to each other then that could create different issues altogether. You would have to ensure that digital logic voltages met the VIL and VIH limits in respect to the switch power supply GND and that it does not exceed the absolute max ratings of the part. This would be difficult if there is no relationship between the two GNDs.
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