TPS54560 EMI issue

Can you provide waveforms of the switch node?  You will need to look for ringing at those specific frequencies.  You may need an RC snubber.  Also, is the inductor a shielded type? You may also want to include some high frequency bypass capacitance on both input and output.   You may also have layout issues.

In addition to Johns comments, a different D5 diode may also improve the performance. In my testing I have had good results with the PDS760.

Dear Sir

May you pls suggest high pass capacitor value in input/output. we will also try it.

Pls refer enclosed files for SW node waveform.

                                       Best regards,

                                                         Bogey

The waveforms you show are the switch node in DCM operation.  That ringing is the result of ringing in the circulating current loop when the inductor current goes to zero.  It is at about 3.2 MHz  I doubt it is related to your 94 MHz issue.  You need to zoom in on the rising edge of the SW node and look at the ringing and overshoot at the top of the pulse.