Sometimes you don't want to bother your customers when you change or upgrade your server how can I change dns name from one server to another? so the customers doesn't have to change the reference in their domain name?

If you are changing the DNS server names that your customers use as the authoritative nameservers for their domains (such as changing from ns1/ns2.yourhost.com to ns1/ns2.yournewname.com), there is nothing you can do to prevent telling them to update their nameserver entries via their domain registrar's website. The only way it is possible is if you happen to own all of their domain names or have access to login to their domain management interface on their domain registrar's website.