I follow the the guide at HowtoForge to install ISPConfig 3 in Ubuntu 9.04. I use server1.example.com as example. After installation, I want to change server1.example.com to my desire domain. But I can't find how to do that.

This is the link to the tutorial:
http://www.howtoforge.com/perfect-se...04-ispconfig-3

Quoting from the link that you gave

"2 Preliminary Note

In this tutorial I use the hostname server1.example.com with the IP address 192.168.0.100 and the gateway 192.168.0.1. These settings might differ for you, so you have to replace them where appropriate."

So, it sounds like the easiest way would be for you to uninstall and reinstall using the hostname and IP address that you need, I am just throwing that out there because I am not familiar at all with that software, just thought I might be able to find something about it online, but after reading that Preliminary Note, I thought maybe they say that because it is either really difficult or impossible to change after the fact.