What is actually happening on rooting? Is it change file system, or modify file or add new files or add new configirations....etc? I know the meaning of rooting but I want to know how it dowing.
When you use your phone, access applications and navigate it's file system, you do so as a user with a given set of permissions. This places certain restrictions on what you can and can't do or access.
Rooting your phone places an executable on your device called su (switch user), this executable switches the account credentials and permissions that you use to interact with the file system on your phone, making you a super user.
Android is based on the Linux Kernel, and this is essentially the same as achieving 'root' on a Linux device (hence the term rooting).
Rooting is a process which gives you full access to all the files on your device allowing you to tweak and customize any element of the Android OS.
Apps like SuperSU are simply security guards which monitor root access and display a window asking you to confirm root access any time an app asks for it.