We maintain our server once a week. Sometimes, the customer wishes that we change some settings which is already cached in server. My colleague always write some JSP code to change these settings which are stored in the memory.
Is it a good method to use this kind of methodology? If our project is not a Web container, which tools can help me?
Usually, in my experience, the server configuration is not stored only in memory of server:
So, usually, people opt for various "externalized configuration" options that can range from "file-based" configuration + redeploy the whole cluster upon each configuration change, to configuration management servers (like Consul, etc.d, etc). There are also some solutions that came from (and used in) a java world: Apache Zookeeper, Spring cloud config server to name a few, there are others. In addition, sometimes, it's convenient to store the configurations in a database.
Now to your question: If your project is not a web container and you don't care that configuration will "disappear" after a server restart and you're not running a distributed cluster of servers, then, using JSP indeed doesn't seem appropriate in this case.
Maybe you should take a look at JMX - Java management extensions, that have a built-in solution so that you probably will be able to get rid of a web container (which seems to be not used by your team anyway other than for JSP modifications that you've described).