how can i transfer library files to xbee 3 cellular flash via serial communication using micropython.

Answer 1

You would need to use the ATFS commands. However these commands are currently not accessible to Micro Python. So I am not sure how else you are going to do it.

https://www.digi.com/resources/documentation/Digidocs/90002219/#reference/r_unavailable_at.htm?Highlight=at%20command

Answer 2

enter command mode by sending +++ over serial port.
Then send AT command:
ATFS PUT filename
Then you can transfer file using ymodem
when done exit command mode by sending AT command:
ATCN