If you have installed YouTrack from EXE Distribution, then the best way to change the database location is by specifying it via JVM property.

1. Stop currently running YouTrack service. Open Control panel > Administrative tools > Services and stop ‘YouTrack Web Server‘ service.
2. In the <YouTrack Installation Directory>/bin start Tomcat‘s service configuration editor by executing the command

   tomcat7w.exe //ES//YouTrack

   

3. Switch to the Java tab and then edit the Java Options (for more information see Tomcat 7 documentation)
4. To change the database location, specify the database.location property:

   -Ddatabase.location=<path to your database>

5. Exit Tomcat‘s service configuration editor.
6. Start ‘YouTrack Web Server‘ service.

【来源】http://confluence.jetbrains.com/display/YTD5/Changing+Database+Location