The Java Organize Import command is overwritten by another Ctrl+Shift+O command: in Window > Preferences: General > Keys the Java Organize Import command (where When is In Windows) is bound to Ctrl+Shift+O, but in the main and right-click menu Source > Organize Imports the command is displayed without the shortcut.
There are two solutions for this problem:
Change or remove the shortcut of the command that overwrites the Java Organize Import command:
Restricts the scope of the shortcut of Java Organize Import to the Java editor:
See also: Spring IDE issue #160: organize imports is not working