How to calculate the loss of TPS54424 when I use it on my design. For example, Vin = 9V, Vo = 3V, Io =3A , fs =500K.
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The efficiency can be estimated from the datasheet, or by using the webench tool. Figure 2 in the datasheet is close to your operating conditions, showing 9Vin to 3.3Vout at 700kHz. Your efficiency will be slightly better because of the lower switching frequency, but slightly worse because of the lower output voltage, but the ~94% shown in the datasheet should be close.
If you want a more detailed estimate, you can use WEBENCH. I did a quick design with your inputs and the results are here: https://webench.ti.com/appinfo/webench/scripts/SDP.cgi?ID=3A367F759B310CB0. WEBENCH shows an efficiency of 93.82%, which is very close to what is shown in the datasheet. Your results may be different due to the inductor you choose.