Structure of payload in data packet when USB initialized as COM port with Serial

I wish to know how this data is structured in payload and how does the baud rate affect this communication or the data

The baud rate doesn't affect this communication it's just sent as an information to the other end to allow to adapt the hardware speed if necessary (p.e. if a FTDI chip is used).

You can find the data structures in the source code delivered with every Arduino IDE. Look at the directory hardware/arduino/core/arduino, the file of most interest is USBCore.h.