IF your website is using cpanel system, your website root directory should be /home/yourusername/public-html directory. When anyone want to visit your website, the apache server will direct it to the index file in your /home/yourusername/public_html folder.
But you can change it to different directory by .htaccess file. Just place following codes into your .htaccess file:
RewriteEngine on
RewriteCond %{HTTP_HOST} ^domain-name.com$ [NC,OR]
RewriteCond %{HTTP_HOST} ^www.domain-name.com$
RewriteCond %{REQUEST_URI} !folder/
RewriteRule (.*) /folder/$1 [L]
In the above lines you should replace the following 2 strings:
domain-name.com – Type your own domain name
folder – custome the folder which hold your website