Inrush current in the Boost Converter during start
This problem is unrelated to the boost-control mechanism/circuit but can be made worse by it if the boost control circuit is activated before the output capacitors are charged to the input supply DC voltage. In other words, it's a regular inrush problem suffered by most circuits that seek to charge high value electrolytic capacitors from a high(ish) supply voltage.

Please suggest me how to solve the problem and what do people do In
practical boost converters?

The problem that you need to overcome is the initial inrush current and this is partially alleviated by R3 being 3 Ω: -

Ignoring the slight reducing-effect that the inductors will have, the inrush current is 200 volts divided by 3 Ω = 66 amps. OK, you are seeing 50 to 60 amps and this is due to the inductors being a reasonable blocking impedance on power up.
If you want to avoid this initial surge then using an NTC thermistor can be a good choice. It has a fairly high initial (cold) resistance (several tens of Ω) dropping to sub Ω values within a few milliseconds as it warms over that short period in time.
Another method is to pre-charge the capacitors to the 200 volt supply voltage prior to switching in the main power circuit. Once the capacitors are charged, you have full control of currents via the boost mechanism.