1. To change the MOTD of the server, open the server.properties file, which is located in the main folder of the server.
2. Search for the "motd" line.
3. You can edit this line to whatever you want, save the file and restart the server. The MOTD should now be updated.

There are also plugins for changing MOTD that bring more features, for example showing the number of players in the MOTD. A popular plugin for MOTDs is ServerListPlus. You can download it from the spigotmc website.