Different buffer size for different serial port of Mega2560 ?

There is no need to change the underlying buffer sizes.

Have a look at the examples in Serial Input Basics - simple reliable ways to receive data.

In the examples the constant numChars sets the size of the array for incoming data to 32. You can easily change that to any size you need. Just use a separate function and a separate set of variables for each of your serial ports.

...R