Added the solution, if anyone is looking for it.

Openupgrade creates a copy of addon in the tmp folder to perform its migration.

Hence first paste the link of custom-addon directory into that tmp folder.(/var/tmp/openupgrade/9.0/)

and then include those custom-addon in the file 'migrate.py'.

migrate.py 

migrations = {
    '9.0': {
        'addons': {
            'addons': {
                'type': 'link',
                'url': os.path.join('server', 'addons'),
            },
            'custom_addons': {
                'type': 'link',
                'url': os.path.join('custom_addons'),
            },
},

Note: If Custom addons exists for former version i.e 8.0 in this case, then the above steps applies for that as well.