When we register DBusObjectPathVTable then who will call the message_function? i.e dbus-daemon will call or the dbus main loop ( _dbus_loop_run function) will call?
libdbus will call members of the DBusObjectPathVTable from the libdbus main loop. You could have checked this yourself by grepping for the members in the libdbus source code: cd dbus.git && git grep message_function shows that dbus/dbus-object-tree.c contains all the calls to it. dbus-object-tree.c is part of libdbus.
It is highly recommended that you use a D-Bus library other than libdbus, however, as libdbus is fiddly to use correctly. If possible, use GDBus or QtDBus instead, as they are much higher-level bindings which are easier to use. If you need a lower-level binding, sd-bus is more modern than libdbus.