will be any problem with my website if I empty all the cache tables from Database?
As per the drupal community doc for clearing the cache you can manually TRUNCATE the tables (empty, not remove) starting with cache_ and there shouldn't be any problem doing so as on visiting any page the cache is rebuilt.

However I would recommend to either use the drush, or clear the cache from the /admin/config/development/performance page.

If you want to clear the cache from code than you may try the following:

// clear cache
drupal_flush_all_caches();


Also its always safe to keep the Backup of database before making any manual operation on database.