@meghdadi To configure the Arduno Zero for crystalless operation, it's necessary to edit line 71 of the SAMD21 core's "boards.txt" file and add the compiler flag -DCRYSTALLESS:
arduino_zero_native.build.extra_flags=-DCRYSTALLESS -D__SAMD21G18A__ {build.usb_flags}
The boards.txt file can be found (on my PC) at:
C:\Users\Computer\AppData\Local\Arduino15\packages\arduino\hardware\samd\1.8.11\