The first part forms a user manual:

Section Installation discusses how to download, compile and install doxygen for your platform.
Section Getting started tells you how to generate your first piece of documentation quickly.
Section Documenting the code demonstrates the various ways that code can be documented.
Section Markdown support show the Markdown formatting supported by doxygen.
Section Lists shows how to create lists.
Section Grouping shows how to group things together.
Section Including formulas shows how to insert formulas in the documentation.
Section Graphs and diagrams describes the diagrams and graphs that doxygen can generate.
Section Preprocessing explains how doxygen deals with macro definitions.
Section Automatic link generation shows how to put links to files, classes, and members in the documentation.
Section Output Formats shows how to generate the various output formats supported by doxygen.
Section Searching shows various ways to search in the HTML documentation.
Section External Indexing and Searching shows how use the external search and index tools
Section Customizing the output explains how you can customize the output generated by doxygen.
Section Custom Commands show how to define and use custom commands in your comments.
Section Linking to external documentation explains how to let doxygen create links to externally generated documentation.
Section Frequently Asked Questions gives answers to frequently asked questions.
Section Troubleshooting tells you what to do when you have problems.

The second part forms a reference manual:

Section Features presents an overview of what doxygen can do.
Section Doxygen usage shows how to use the doxygen program.
Section Doxywizard usage shows how to use the doxywizard program.
Section Configuration shows how to fine-tune doxygen, so it generates the documentation you want.
Section Special Commands shows an overview of the special commands that can be used within the documentation.
Section HTML Commands shows an overview of the HTML commands that can be used within the documentation.
Section XML Commands shows an overview of the C# style XML commands that can be used within the documentation.

The third part provides information for developers:

Section Doxygen's Internals gives a global overview of how doxygen is internally structured.
Section Perl Module Output shows how to use the PerlMod output.
Section Internationalization explains how to add support for new output languages.