As JKSH said, plus:
qdoc does not guarantee it's API, it is being modified between Qt releases and can simply break without notice
doxygen supports just soo much more: aparat from C++ and Qt with all it's features (including QML), it also understands Java, JavaScript and many others. It also supports different comment styles, and can produce much more output formats than qdoc (HTML, PDF, man pages, LaTeX, etc.)